PDB Short entry for 2VX1 HEADER TRANSFERASE 30-JUN-08 2VX1 TITLE EPHB4 KINASE DOMAIN INHIBITOR COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPHRIN TYPE-B RECEPTOR 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN, RESIDUES 598-899; COMPND 5 SYNONYM: TYROSINE-PROTEIN KINASE RECEPTOR HTK, TYROSINE-PROTEIN COMPND 6 KINASE TYRO11, EPHB4 RECEPTOR TYROSINE KINASE; COMPND 7 EC: 2.7.10.1; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: SF21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PFASTBAC KEYWDS TYROSINE-PROTEIN KINASE, RECEPTOR TYROSINE KINASE, KINASE, MUTANT, KEYWDS 2 MEMBRANE, RECEPTOR, TRANSFERASE, ATP-BINDING, POLYMORPHISM, KEYWDS 3 GLYCOPROTEIN, TRANSMEMBRANE, PHOSPHOPROTEIN, UNPHOSPHORYLATED, KEYWDS 4 NUCLEOTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.READ,C.A.BRASSINGTON,I.GREEN,E.J.MCCALL,A.L.VALENTINE,D.BARRATT, AUTHOR 2 A.G.LEACH,J.G.KETTLE REVDAT 8 13-DEC-23 2VX1 1 REMARK LINK REVDAT 7 08-MAY-19 2VX1 1 REMARK REVDAT 6 24-APR-19 2VX1 1 SOURCE REVDAT 5 28-JUN-17 2VX1 1 REMARK REVDAT 4 10-NOV-09 2VX1 1 JRNL REMARK SITE REVDAT 3 24-FEB-09 2VX1 1 SEQADV REVDAT 2 23-DEC-08 2VX1 1 VERSN JRNL REVDAT 1 28-OCT-08 2VX1 0 JRNL AUTH C.BARDELLE,T.COLEMAN,D.CROSS,S.DAVENPORT,J.G.KETTLE,E.J.KO, JRNL AUTH 2 A.G.LEACH,A.MORTLOCK,J.READ,N.J.ROBERTS,P.ROBINS, JRNL AUTH 3 E.J.WILLIAMS JRNL TITL INHIBITORS OF THE TYROSINE KINASE EPHB4. PART 2: JRNL TITL 2 STRUCTURE-BASED DISCOVERY AND OPTIMISATION OF 3,5-BIS JRNL TITL 3 SUBSTITUTED ANILINOPYRIMIDINES. JRNL REF BIOORG.MED.CHEM.LETT. V. 18 5717 2008 JRNL REFN ISSN 0960-894X JRNL PMID 18851911 JRNL DOI 10.1016/J.BMCL.2008.09.087 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.BARDELLE,D.CROSS,S.DAVENPORT,J.G.KETTLE,E.J.KO,A.G.LEACH, REMARK 1 AUTH 2 A.MORTLOCK,J.READ,N.J.ROBERTS,P.ROBINS,E.J.WILLIAMS REMARK 1 TITL INHIBITORS OF THE TYROSINE KINASE EPHB4. PART 1: REMARK 1 TITL 2 STRUCTURE-BASED DESIGN AND OPTIMIZATION OF A SERIES OF REMARK 1 TITL 3 2,4-BIS-ANILINOPYRIMIDINES REMARK 1 REF BIOORG.MED.CHEM.LETT. V. 18 2776 2008 REMARK 1 REFN ISSN 0960-894X REMARK 1 PMID 18434142 REMARK 1 DOI 10.1016/J.BMCL.2008.04.015 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 85.2 REMARK 3 NUMBER OF REFLECTIONS : 27330 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1464 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 574 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 31 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2123 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.23000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.53000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.114 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.852 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2275 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2066 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3079 ; 1.469 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4805 ; 0.812 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 280 ; 5.485 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 104 ;36.594 ;23.558 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 402 ;12.041 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;14.609 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 329 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2582 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 461 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 495 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2108 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1125 ; 0.186 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1259 ; 0.080 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 160 ; 0.166 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 5 ; 0.091 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 40 ; 0.259 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.168 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1495 ; 0.972 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2224 ; 1.348 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1010 ; 2.170 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 851 ; 3.149 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2VX1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1290036731. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU-MSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28794 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.2 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 27.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.96 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2VWU REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 12MG/ML IN 50MM MOPS PH 6.5, REMARK 280 50MM NACL, 1MM DTT RESERVOIR: 25% PEG 5000 MME, 0.1M TRIS PH 7.5, REMARK 280 0.15M MGCL2, 15% GLYCEROL TEMP: 18 DEGREES C SITTING DROP: 2 UL REMARK 280 PROTEIN, 0.6 UL RESERVOIR, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.76850 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLU 774 TO TYR 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 ASP A 598 REMARK 465 PRO A 599 REMARK 465 ASN A 600 REMARK 465 GLU A 601 REMARK 465 ALA A 602 REMARK 465 VAL A 603 REMARK 465 ARG A 604 REMARK 465 GLU A 605 REMARK 465 PHE A 606 REMARK 465 ALA A 607 REMARK 465 PRO A 772 REMARK 465 THR A 773 REMARK 465 GLU A 774 REMARK 465 THR A 775 REMARK 465 SER A 776 REMARK 465 SER A 777 REMARK 465 LEU A 778 REMARK 465 ARG A 889 REMARK 465 GLU A 890 REMARK 465 ASN A 891 REMARK 465 GLY A 892 REMARK 465 GLY A 893 REMARK 465 ALA A 894 REMARK 465 SER A 895 REMARK 465 HIS A 896 REMARK 465 PRO A 897 REMARK 465 LEU A 898 REMARK 465 LEU A 899 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 616 CD CE NZ REMARK 470 ARG A 633 CZ NH1 NH2 REMARK 470 LYS A 639 CD CE NZ REMARK 470 LYS A 640 CD CE NZ REMARK 470 ARG A 656 CD NE CZ NH1 NH2 REMARK 470 ARG A 659 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 765 CG CD1 CD2 REMARK 470 LYS A 781 CD CE NZ REMARK 470 ARG A 795 NE CZ NH1 NH2 REMARK 470 ARG A 866 CZ NH1 NH2 REMARK 470 LYS A 876 CD CE NZ REMARK 470 ARG A 879 CD NE REMARK 470 LYS A 885 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2093 O HOH A 2107 2655 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 739 -12.84 77.96 REMARK 500 ASP A 758 88.46 80.46 REMARK 500 ASN A 768 -161.01 -105.29 REMARK 500 SER A 770 -47.53 -26.42 REMARK 500 TRP A 822 -120.30 40.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1890 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 740 OD2 REMARK 620 2 ASP A 758 OD1 93.0 REMARK 620 3 HOH A2116 O 93.3 173.6 REMARK 620 4 HOH A2129 O 175.8 84.7 89.1 REMARK 620 5 HOH A2130 O 95.6 90.6 87.6 87.9 REMARK 620 6 HOH A2131 O 90.2 91.1 90.1 86.3 173.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1891 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2114 O REMARK 620 2 HOH A2128 O 89.1 REMARK 620 3 HOH A2130 O 103.5 103.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1892 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2088 O REMARK 620 2 HOH A2089 O 86.4 REMARK 620 3 HOH A2168 O 174.8 91.4 REMARK 620 4 HOH A2169 O 88.4 96.8 87.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 7X8 A 1889 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1890 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1891 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1892 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BBA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE AND THERMODYNAMIC CHARACTERIZATION OF THEEPHB4 REMARK 900 RECEPTOR IN COMPLEX WITH AN EPHRIN-B2 ANTAGONISTPEPTIDE REVEALS THE REMARK 900 DETERMINANTS FOR RECEPTOR SPECIFICITY REMARK 900 RELATED ID: 2VWU RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2VWV RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2VWY RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2VWW RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2VWX RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2VWZ RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 900 RELATED ID: 2VX0 RELATED DB: PDB REMARK 900 EPHB4 KINASE DOMAIN INHIBITOR COMPLEX REMARK 999 REMARK 999 SEQUENCE REMARK 999 Y774E MUTATION NOT SEEN IN ELECTRON DENSITY DBREF 2VX1 A 598 899 UNP P54760 EPHB4_HUMAN 598 899 SEQADV 2VX1 GLU A 774 UNP P54760 TYR 774 ENGINEERED MUTATION SEQRES 1 A 302 ASP PRO ASN GLU ALA VAL ARG GLU PHE ALA LYS GLU ILE SEQRES 2 A 302 ASP VAL SER TYR VAL LYS ILE GLU GLU VAL ILE GLY ALA SEQRES 3 A 302 GLY GLU PHE GLY GLU VAL CYS ARG GLY ARG LEU LYS ALA SEQRES 4 A 302 PRO GLY LYS LYS GLU SER CYS VAL ALA ILE LYS THR LEU SEQRES 5 A 302 LYS GLY GLY TYR THR GLU ARG GLN ARG ARG GLU PHE LEU SEQRES 6 A 302 SER GLU ALA SER ILE MET GLY GLN PHE GLU HIS PRO ASN SEQRES 7 A 302 ILE ILE ARG LEU GLU GLY VAL VAL THR ASN SER MET PRO SEQRES 8 A 302 VAL MET ILE LEU THR GLU PHE MET GLU ASN GLY ALA LEU SEQRES 9 A 302 ASP SER PHE LEU ARG LEU ASN ASP GLY GLN PHE THR VAL SEQRES 10 A 302 ILE GLN LEU VAL GLY MET LEU ARG GLY ILE ALA SER GLY SEQRES 11 A 302 MET ARG TYR LEU ALA GLU MET SER TYR VAL HIS ARG ASP SEQRES 12 A 302 LEU ALA ALA ARG ASN ILE LEU VAL ASN SER ASN LEU VAL SEQRES 13 A 302 CYS LYS VAL SER ASP PHE GLY LEU SER ARG PHE LEU GLU SEQRES 14 A 302 GLU ASN SER SER ASP PRO THR GLU THR SER SER LEU GLY SEQRES 15 A 302 GLY LYS ILE PRO ILE ARG TRP THR ALA PRO GLU ALA ILE SEQRES 16 A 302 ALA PHE ARG LYS PHE THR SER ALA SER ASP ALA TRP SER SEQRES 17 A 302 TYR GLY ILE VAL MET TRP GLU VAL MET SER PHE GLY GLU SEQRES 18 A 302 ARG PRO TYR TRP ASP MET SER ASN GLN ASP VAL ILE ASN SEQRES 19 A 302 ALA ILE GLU GLN ASP TYR ARG LEU PRO PRO PRO PRO ASP SEQRES 20 A 302 CYS PRO THR SER LEU HIS GLN LEU MET LEU ASP CYS TRP SEQRES 21 A 302 GLN LYS ASP ARG ASN ALA ARG PRO ARG PHE PRO GLN VAL SEQRES 22 A 302 VAL SER ALA LEU ASP LYS MET ILE ARG ASN PRO ALA SER SEQRES 23 A 302 LEU LYS ILE VAL ALA ARG GLU ASN GLY GLY ALA SER HIS SEQRES 24 A 302 PRO LEU LEU HET 7X8 A1889 36 HET MG A1890 1 HET MG A1891 1 HET MG A1892 1 HETNAM 7X8 3-({4-[(5-CHLORO-1,3-BENZODIOXOL-4-YL)AMINO]PYRIMIDIN- HETNAM 2 7X8 2-YL}AMINO)BENZAMIDE HETNAM MG MAGNESIUM ION FORMUL 2 7X8 C18 H14 CL N5 O3 FORMUL 3 MG 3(MG 2+) FORMUL 6 HOH *260(H2 O) HELIX 1 1 ASP A 611 SER A 613 5 3 HELIX 2 2 THR A 654 GLY A 669 1 16 HELIX 3 3 ALA A 700 ASN A 708 1 9 HELIX 4 4 THR A 713 MET A 734 1 22 HELIX 5 5 ALA A 742 ARG A 744 5 3 HELIX 6 6 PHE A 764 ASN A 768 5 5 HELIX 7 7 PRO A 783 THR A 787 5 5 HELIX 8 8 ALA A 788 ARG A 795 1 8 HELIX 9 9 THR A 798 SER A 815 1 18 HELIX 10 10 SER A 825 GLN A 835 1 11 HELIX 11 11 PRO A 846 TRP A 857 1 12 HELIX 12 12 ASP A 860 ARG A 864 5 5 HELIX 13 13 ARG A 866 ASN A 880 1 15 HELIX 14 14 PRO A 881 ILE A 886 5 6 SHEET 1 AA 5 VAL A 615 ALA A 623 0 SHEET 2 AA 5 GLU A 628 LEU A 634 -1 O VAL A 629 N ILE A 621 SHEET 3 AA 5 SER A 642 LEU A 649 -1 O SER A 642 N LEU A 634 SHEET 4 AA 5 VAL A 689 GLU A 694 -1 O VAL A 689 N LEU A 649 SHEET 5 AA 5 LEU A 679 VAL A 683 -1 N GLU A 680 O LEU A 692 SHEET 1 AB 2 ILE A 746 VAL A 748 0 SHEET 2 AB 2 CYS A 754 VAL A 756 -1 O LYS A 755 N LEU A 747 LINK OD2 ASP A 740 MG MG A1890 1555 1555 2.09 LINK OD1 ASP A 758 MG MG A1890 1555 1555 2.03 LINK MG MG A1890 O HOH A2116 1555 1555 2.05 LINK MG MG A1890 O HOH A2129 1555 1555 2.14 LINK MG MG A1890 O HOH A2130 1555 1555 2.10 LINK MG MG A1890 O HOH A2131 1555 1555 2.13 LINK MG MG A1891 O HOH A2114 1555 1555 1.79 LINK MG MG A1891 O HOH A2128 1555 1555 1.82 LINK MG MG A1891 O HOH A2130 1555 1555 1.52 LINK MG MG A1892 O HOH A2088 1555 1555 2.12 LINK MG MG A1892 O HOH A2089 1555 1555 2.07 LINK MG MG A1892 O HOH A2168 1555 1555 2.05 LINK MG MG A1892 O HOH A2169 1555 1555 2.06 CISPEP 1 MET A 687 PRO A 688 0 1.02 SITE 1 AC1 16 ILE A 621 GLY A 622 ALA A 645 LYS A 647 SITE 2 AC1 16 GLU A 664 ILE A 691 THR A 693 GLU A 694 SITE 3 AC1 16 MET A 696 GLU A 697 GLY A 699 LEU A 747 SITE 4 AC1 16 HOH A2256 HOH A2257 HOH A2258 HOH A2259 SITE 1 AC2 7 ASP A 740 ASP A 758 MG A1891 HOH A2116 SITE 2 AC2 7 HOH A2129 HOH A2130 HOH A2131 SITE 1 AC3 6 ASP A 740 ASP A 758 MG A1890 HOH A2114 SITE 2 AC3 6 HOH A2128 HOH A2130 SITE 1 AC4 4 HOH A2088 HOH A2089 HOH A2168 HOH A2169 CRYST1 46.116 53.537 61.505 90.00 110.90 90.00 P 1 21 1 2 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 0.021684 0.000000 0.008280 0.00000 SCALE2 0.000000 0.018679 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017404 0.00000