PDB Short entry for 3G0F HEADER TRANSFERASE 27-JAN-09 3G0F TITLE KIT KINASE DOMAIN MUTANT D816H IN COMPLEX WITH SUNITINIB COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAST/STEM CELL GROWTH FACTOR RECEPTOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: KINASE DOMAIN - KID DELETED; COMPND 5 SYNONYM: SCFR, PROTO-ONCOGENE TYROSINE-PROTEIN KINASE KIT, C-KIT; COMPND 6 EC: 2.7.10.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KIT; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VIRUS KEYWDS KIT KINASE DOMAIN, SUTENT BINDING, DRUG RESISTANCE, ATP-BINDING, KEYWDS 2 DISEASE MUTATION, GLYCOPROTEIN, IMMUNOGLOBULIN DOMAIN, KINASE, KEYWDS 3 MEMBRANE, NUCLEOTIDE-BINDING, PHOSPHOPROTEIN, POLYMORPHISM, PROTO- KEYWDS 4 ONCOGENE, RECEPTOR, TRANSMEMBRANE, TYROSINE-PROTEIN KINASE, KEYWDS 5 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.S.GAJIWALA,J.C.WU,E.A.LUNNEY,G.D.DEMETRI REVDAT 6 03-APR-24 3G0F 1 REMARK REVDAT 5 29-NOV-23 3G0F 1 REMARK REVDAT 4 20-OCT-21 3G0F 1 COMPND REMARK SEQADV HETNAM REVDAT 3 16-AUG-17 3G0F 1 SOURCE REMARK REVDAT 2 13-OCT-09 3G0F 1 JRNL REVDAT 1 24-FEB-09 3G0F 0 JRNL AUTH K.S.GAJIWALA,J.C.WU,J.CHRISTENSEN,G.D.DESHMUKH,W.DIEHL, JRNL AUTH 2 J.P.DINITTO,J.M.ENGLISH,M.J.GREIG,Y.A.HE,S.L.JACQUES, JRNL AUTH 3 E.A.LUNNEY,M.MCTIGUE,D.MOLINA,T.QUENZER,P.A.WELLS,X.YU, JRNL AUTH 4 Y.ZHANG,A.ZOU,M.R.EMMETT,A.G.MARSHALL,H.M.ZHANG,G.D.DEMETRI JRNL TITL KIT KINASE MUTANTS SHOW UNIQUE MECHANISMS OF DRUG RESISTANCE JRNL TITL 2 TO IMATINIB AND SUNITINIB IN GASTROINTESTINAL STROMAL TUMOR JRNL TITL 3 PATIENTS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 1542 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19164557 JRNL DOI 10.1073/PNAS.0812413106 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 25905 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1307 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 26921 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE : 0.3160 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 205 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4658 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 15 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.30 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.36 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.660 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3G0F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051265. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 98 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26751 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : 0.04200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.21600 REMARK 200 R SYM FOR SHELL (I) : 0.21600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNX REMARK 200 STARTING MODEL: SUNITINIB BOUND WILD-TYPE KINASE DOMAIN OF KIT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM SULFATE, 286K, PH 7, REMARK 280 VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 39.73100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.89150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.73100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.89150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 48470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 203.56600 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 542 REMARK 465 PRO A 543 REMARK 465 THR A 544 REMARK 465 TYR A 545 REMARK 465 LYS A 546 REMARK 465 TYR A 547 REMARK 465 LEU A 548 REMARK 465 GLN A 549 REMARK 465 LYS A 550 REMARK 465 PRO A 551 REMARK 465 MET A 552 REMARK 465 TYR A 553 REMARK 465 GLU A 554 REMARK 465 VAL A 555 REMARK 465 GLN A 556 REMARK 465 TRP A 557 REMARK 465 LYS A 558 REMARK 465 VAL A 559 REMARK 465 VAL A 560 REMARK 465 GLU A 561 REMARK 465 GLU A 562 REMARK 465 ILE A 563 REMARK 465 ASN A 564 REMARK 465 GLY A 565 REMARK 465 ILE A 690 REMARK 465 CYS A 691 REMARK 465 SER A 692 REMARK 465 LYS A 693 REMARK 465 THR A 694 REMARK 465 SER A 753 REMARK 465 PRO A 754 REMARK 465 ALA A 755 REMARK 465 ILE A 756 REMARK 465 MET A 757 REMARK 465 GLU A 758 REMARK 465 ASP A 759 REMARK 465 ASP A 760 REMARK 465 GLU A 761 REMARK 465 LEU A 762 REMARK 465 ALA A 763 REMARK 465 SER A 931 REMARK 465 THR A 932 REMARK 465 ASN A 933 REMARK 465 HIS A 934 REMARK 465 ILE A 935 REMARK 465 GLY B 542 REMARK 465 PRO B 543 REMARK 465 THR B 544 REMARK 465 TYR B 545 REMARK 465 LYS B 546 REMARK 465 TYR B 547 REMARK 465 LEU B 548 REMARK 465 GLN B 549 REMARK 465 LYS B 550 REMARK 465 PRO B 551 REMARK 465 MET B 552 REMARK 465 TYR B 553 REMARK 465 GLU B 554 REMARK 465 VAL B 555 REMARK 465 GLN B 556 REMARK 465 TRP B 557 REMARK 465 LYS B 558 REMARK 465 VAL B 559 REMARK 465 VAL B 560 REMARK 465 GLU B 561 REMARK 465 GLU B 562 REMARK 465 ILE B 563 REMARK 465 ILE B 690 REMARK 465 CYS B 691 REMARK 465 SER B 692 REMARK 465 LYS B 693 REMARK 465 THR B 694 REMARK 465 SER B 753 REMARK 465 PRO B 754 REMARK 465 ALA B 755 REMARK 465 ILE B 756 REMARK 465 MET B 757 REMARK 465 GLU B 758 REMARK 465 ASP B 759 REMARK 465 ASP B 760 REMARK 465 GLU B 761 REMARK 465 LEU B 762 REMARK 465 ALA B 763 REMARK 465 SER B 931 REMARK 465 THR B 932 REMARK 465 ASN B 933 REMARK 465 HIS B 934 REMARK 465 ILE B 935 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ILE A 612 -64.98 -98.65 REMARK 500 ASP A 792 46.55 -159.59 REMARK 500 LEU A 813 -10.91 78.50 REMARK 500 PHE A 842 -92.65 -80.74 REMARK 500 ASN A 843 2.15 -63.41 REMARK 500 TYR A 870 62.71 39.95 REMARK 500 LYS A 926 -39.67 -137.62 REMARK 500 GLN A 927 10.54 -56.05 REMARK 500 ASN B 566 96.81 65.72 REMARK 500 LEU B 576 153.85 171.33 REMARK 500 PRO B 627 1.89 -59.68 REMARK 500 ASP B 792 50.39 -153.63 REMARK 500 LEU B 813 -27.30 76.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 B49 A 9001 REMARK 610 B49 B 9001 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B49 A9001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B49 B9001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3G0E RELATED DB: PDB REMARK 900 KIT KINASE DOMAIN IN COMPLEX WITH SUNITINIB REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 694-753 DELETED, REPLACED WITH TS DBREF 3G0F A 544 693 UNP P10721 KIT_HUMAN 544 693 DBREF 3G0F A 754 935 UNP P10721 KIT_HUMAN 754 935 DBREF 3G0F B 544 693 UNP P10721 KIT_HUMAN 544 693 DBREF 3G0F B 754 935 UNP P10721 KIT_HUMAN 754 935 SEQADV 3G0F GLY A 542 UNP P10721 EXPRESSION TAG SEQADV 3G0F PRO A 543 UNP P10721 EXPRESSION TAG SEQADV 3G0F THR A 694 UNP P10721 SEE REMARK 999 SEQADV 3G0F SER A 753 UNP P10721 SEE REMARK 999 SEQADV 3G0F HIS A 816 UNP P10721 ASP 816 ENGINEERED MUTATION SEQADV 3G0F GLY B 542 UNP P10721 EXPRESSION TAG SEQADV 3G0F PRO B 543 UNP P10721 EXPRESSION TAG SEQADV 3G0F THR B 694 UNP P10721 SEE REMARK 999 SEQADV 3G0F SER B 753 UNP P10721 SEE REMARK 999 SEQADV 3G0F HIS B 816 UNP P10721 ASP 816 ENGINEERED MUTATION SEQRES 1 A 336 GLY PRO THR TYR LYS TYR LEU GLN LYS PRO MET TYR GLU SEQRES 2 A 336 VAL GLN TRP LYS VAL VAL GLU GLU ILE ASN GLY ASN ASN SEQRES 3 A 336 TYR VAL TYR ILE ASP PRO THR GLN LEU PRO TYR ASP HIS SEQRES 4 A 336 LYS TRP GLU PHE PRO ARG ASN ARG LEU SER PHE GLY LYS SEQRES 5 A 336 THR LEU GLY ALA GLY ALA PHE GLY LYS VAL VAL GLU ALA SEQRES 6 A 336 THR ALA TYR GLY LEU ILE LYS SER ASP ALA ALA MET THR SEQRES 7 A 336 VAL ALA VAL LYS MET LEU LYS PRO SER ALA HIS LEU THR SEQRES 8 A 336 GLU ARG GLU ALA LEU MET SER GLU LEU LYS VAL LEU SER SEQRES 9 A 336 TYR LEU GLY ASN HIS MET ASN ILE VAL ASN LEU LEU GLY SEQRES 10 A 336 ALA CYS THR ILE GLY GLY PRO THR LEU VAL ILE THR GLU SEQRES 11 A 336 TYR CYS CYS TYR GLY ASP LEU LEU ASN PHE LEU ARG ARG SEQRES 12 A 336 LYS ARG ASP SER PHE ILE CYS SER LYS THR SER PRO ALA SEQRES 13 A 336 ILE MET GLU ASP ASP GLU LEU ALA LEU ASP LEU GLU ASP SEQRES 14 A 336 LEU LEU SER PHE SER TYR GLN VAL ALA LYS GLY MET ALA SEQRES 15 A 336 PHE LEU ALA SER LYS ASN CYS ILE HIS ARG ASP LEU ALA SEQRES 16 A 336 ALA ARG ASN ILE LEU LEU THR HIS GLY ARG ILE THR LYS SEQRES 17 A 336 ILE CYS ASP PHE GLY LEU ALA ARG HIS ILE LYS ASN ASP SEQRES 18 A 336 SER ASN TYR VAL VAL LYS GLY ASN ALA ARG LEU PRO VAL SEQRES 19 A 336 LYS TRP MET ALA PRO GLU SER ILE PHE ASN CYS VAL TYR SEQRES 20 A 336 THR PHE GLU SER ASP VAL TRP SER TYR GLY ILE PHE LEU SEQRES 21 A 336 TRP GLU LEU PHE SER LEU GLY SER SER PRO TYR PRO GLY SEQRES 22 A 336 MET PRO VAL ASP SER LYS PHE TYR LYS MET ILE LYS GLU SEQRES 23 A 336 GLY PHE ARG MET LEU SER PRO GLU HIS ALA PRO ALA GLU SEQRES 24 A 336 MET TYR ASP ILE MET LYS THR CYS TRP ASP ALA ASP PRO SEQRES 25 A 336 LEU LYS ARG PRO THR PHE LYS GLN ILE VAL GLN LEU ILE SEQRES 26 A 336 GLU LYS GLN ILE SER GLU SER THR ASN HIS ILE SEQRES 1 B 336 GLY PRO THR TYR LYS TYR LEU GLN LYS PRO MET TYR GLU SEQRES 2 B 336 VAL GLN TRP LYS VAL VAL GLU GLU ILE ASN GLY ASN ASN SEQRES 3 B 336 TYR VAL TYR ILE ASP PRO THR GLN LEU PRO TYR ASP HIS SEQRES 4 B 336 LYS TRP GLU PHE PRO ARG ASN ARG LEU SER PHE GLY LYS SEQRES 5 B 336 THR LEU GLY ALA GLY ALA PHE GLY LYS VAL VAL GLU ALA SEQRES 6 B 336 THR ALA TYR GLY LEU ILE LYS SER ASP ALA ALA MET THR SEQRES 7 B 336 VAL ALA VAL LYS MET LEU LYS PRO SER ALA HIS LEU THR SEQRES 8 B 336 GLU ARG GLU ALA LEU MET SER GLU LEU LYS VAL LEU SER SEQRES 9 B 336 TYR LEU GLY ASN HIS MET ASN ILE VAL ASN LEU LEU GLY SEQRES 10 B 336 ALA CYS THR ILE GLY GLY PRO THR LEU VAL ILE THR GLU SEQRES 11 B 336 TYR CYS CYS TYR GLY ASP LEU LEU ASN PHE LEU ARG ARG SEQRES 12 B 336 LYS ARG ASP SER PHE ILE CYS SER LYS THR SER PRO ALA SEQRES 13 B 336 ILE MET GLU ASP ASP GLU LEU ALA LEU ASP LEU GLU ASP SEQRES 14 B 336 LEU LEU SER PHE SER TYR GLN VAL ALA LYS GLY MET ALA SEQRES 15 B 336 PHE LEU ALA SER LYS ASN CYS ILE HIS ARG ASP LEU ALA SEQRES 16 B 336 ALA ARG ASN ILE LEU LEU THR HIS GLY ARG ILE THR LYS SEQRES 17 B 336 ILE CYS ASP PHE GLY LEU ALA ARG HIS ILE LYS ASN ASP SEQRES 18 B 336 SER ASN TYR VAL VAL LYS GLY ASN ALA ARG LEU PRO VAL SEQRES 19 B 336 LYS TRP MET ALA PRO GLU SER ILE PHE ASN CYS VAL TYR SEQRES 20 B 336 THR PHE GLU SER ASP VAL TRP SER TYR GLY ILE PHE LEU SEQRES 21 B 336 TRP GLU LEU PHE SER LEU GLY SER SER PRO TYR PRO GLY SEQRES 22 B 336 MET PRO VAL ASP SER LYS PHE TYR LYS MET ILE LYS GLU SEQRES 23 B 336 GLY PHE ARG MET LEU SER PRO GLU HIS ALA PRO ALA GLU SEQRES 24 B 336 MET TYR ASP ILE MET LYS THR CYS TRP ASP ALA ASP PRO SEQRES 25 B 336 LEU LYS ARG PRO THR PHE LYS GLN ILE VAL GLN LEU ILE SEQRES 26 B 336 GLU LYS GLN ILE SER GLU SER THR ASN HIS ILE HET B49 A9001 22 HET SO4 A 1 5 HET B49 B9001 22 HETNAM B49 N-[2-(DIETHYLAMINO)ETHYL]-5-[(Z)-(5-FLUORO-2-OXO-1,2- HETNAM 2 B49 DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-2,4-DIMETHYL-1H- HETNAM 3 B49 PYRROLE-3-CARBO XAMIDE HETNAM SO4 SULFATE ION HETSYN B49 SUNITINIB FORMUL 3 B49 2(C22 H27 F N4 O2) FORMUL 4 SO4 O4 S 2- FORMUL 6 HOH *15(H2 O) HELIX 1 1 ASP A 579 GLU A 583 5 5 HELIX 2 2 PRO A 585 ASN A 587 5 3 HELIX 3 3 HIS A 630 GLY A 648 1 19 HELIX 4 4 LEU A 678 LYS A 685 1 8 HELIX 5 5 ASP A 765 LYS A 786 1 22 HELIX 6 6 ALA A 794 ARG A 796 5 3 HELIX 7 7 HIS A 802 ARG A 804 5 3 HELIX 8 8 PRO A 832 MET A 836 5 5 HELIX 9 9 ALA A 837 PHE A 842 1 6 HELIX 10 10 THR A 847 SER A 864 1 18 HELIX 11 11 ASP A 876 GLU A 885 1 10 HELIX 12 12 PRO A 896 TRP A 907 1 12 HELIX 13 13 THR A 916 GLU A 925 1 10 HELIX 14 14 ASP B 579 GLU B 583 5 5 HELIX 15 15 PRO B 585 ASN B 587 5 3 HELIX 16 16 HIS B 630 GLY B 648 1 19 HELIX 17 17 LEU B 678 LYS B 685 1 8 HELIX 18 18 ASP B 765 LYS B 786 1 22 HELIX 19 19 ALA B 794 ARG B 796 5 3 HELIX 20 20 HIS B 802 ARG B 804 5 3 HELIX 21 21 PRO B 832 MET B 836 5 5 HELIX 22 22 ALA B 837 ASN B 843 1 7 HELIX 23 23 THR B 847 SER B 864 1 18 HELIX 24 24 ASP B 876 GLY B 886 1 11 HELIX 25 25 PRO B 896 TRP B 907 1 12 HELIX 26 26 ASP B 910 ARG B 914 5 5 HELIX 27 27 THR B 916 GLN B 927 1 12 SHEET 1 A 2 TYR A 568 TYR A 570 0 SHEET 2 A 2 CYS B 788 HIS B 790 -1 O ILE B 789 N VAL A 569 SHEET 1 B 5 LEU A 589 ALA A 597 0 SHEET 2 B 5 GLY A 601 TYR A 609 -1 O GLU A 605 N GLY A 592 SHEET 3 B 5 ALA A 617 LEU A 625 -1 O VAL A 622 N VAL A 604 SHEET 4 B 5 LEU A 667 GLU A 671 -1 O THR A 670 N ALA A 621 SHEET 5 B 5 LEU A 656 CYS A 660 -1 N LEU A 657 O ILE A 669 SHEET 1 C 3 GLY A 676 ASP A 677 0 SHEET 2 C 3 ILE A 798 LEU A 800 -1 O LEU A 800 N GLY A 676 SHEET 3 C 3 THR A 806 ILE A 808 -1 O LYS A 807 N LEU A 799 SHEET 1 D 2 CYS A 788 HIS A 790 0 SHEET 2 D 2 TYR B 568 TYR B 570 -1 O VAL B 569 N ILE A 789 SHEET 1 E 2 VAL A 824 LYS A 826 0 SHEET 2 E 2 ALA A 829 LEU A 831 -1 O LEU A 831 N VAL A 824 SHEET 1 F 5 LEU B 589 ALA B 597 0 SHEET 2 F 5 GLY B 601 ILE B 612 -1 O VAL B 603 N GLY B 596 SHEET 3 F 5 ASP B 615 LEU B 625 -1 O VAL B 622 N VAL B 604 SHEET 4 F 5 LEU B 667 GLU B 671 -1 O THR B 670 N ALA B 621 SHEET 5 F 5 LEU B 656 CYS B 660 -1 N LEU B 657 O ILE B 669 SHEET 1 G 3 GLY B 676 ASP B 677 0 SHEET 2 G 3 ILE B 798 LEU B 800 -1 O LEU B 800 N GLY B 676 SHEET 3 G 3 THR B 806 ILE B 808 -1 O LYS B 807 N LEU B 799 SHEET 1 H 2 VAL B 824 LYS B 826 0 SHEET 2 H 2 ALA B 829 LEU B 831 -1 O LEU B 831 N VAL B 824 SITE 1 AC1 9 VAL A 603 ALA A 621 THR A 670 GLU A 671 SITE 2 AC1 9 TYR A 672 CYS A 673 CYS A 674 LEU A 799 SITE 3 AC1 9 CYS A 809 SITE 1 AC2 5 HIS A 630 LEU A 631 ARG A 634 LYS B 826 SITE 2 AC2 5 GLY B 827 SITE 1 AC3 12 LEU B 595 VAL B 603 ALA B 621 THR B 670 SITE 2 AC3 12 GLU B 671 TYR B 672 CYS B 673 GLY B 676 SITE 3 AC3 12 LEU B 799 CYS B 809 ASP B 810 PHE B 811 CRYST1 79.462 101.783 105.505 90.00 90.00 90.00 P 21 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012585 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009825 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009478 0.00000