PDB Short entry for 2XNP HEADER TRANSFERASE 05-AUG-10 2XNP TITLE STRUCTURE OF NEK2 BOUND TO CCT244858 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE NEK2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN, RESIDUES 1-271; COMPND 5 SYNONYM: NEVER IN MITOSIS A-RELATED KINASE 2, NEK2, NIMA-RELATED COMPND 6 PROTEIN KINASE 2, NIMA-LIKE PROTEIN KINASE 1, HSPK 21; COMPND 7 EC: 2.7.11.1; COMPND 8 ENGINEERED: 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: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET30 KEYWDS TRANSFERASE, CENTROSOME, MITOSIS, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR C.MAS-DROUX,R.BAYLISS REVDAT 2 20-DEC-23 2XNP 1 REMARK REVDAT 1 30-MAR-11 2XNP 0 JRNL AUTH S.SOLANKI,P.INNOCENTI,C.MAS-DROUX,K.BOXALL,C.BARILLARI, JRNL AUTH 2 R.L.VAN MONTFORT,G.W.AHERNE,R.BAYLISS,S.HOELDER JRNL TITL BENZIMIDAZOLE INHIBITORS INDUCE A DFG-OUT CONFORMATION OF JRNL TITL 2 NEVER IN MITOSIS GENE A-RELATED KINASE 2 (NEK2) WITHOUT JRNL TITL 3 BINDING TO THE BACK POCKET AND REVEAL A NONLINEAR JRNL TITL 4 STRUCTURE-ACTIVITY RELATIONSHIP. JRNL REF J.MED.CHEM. V. 54 1626 2011 JRNL REFN ISSN 0022-2623 JRNL PMID 21366329 JRNL DOI 10.1021/JM1011726 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 22973 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1165 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 36.7904 - 3.9586 0.98 2802 182 0.1670 0.1908 REMARK 3 2 3.9586 - 3.1426 0.99 2789 138 0.1449 0.1816 REMARK 3 3 3.1426 - 2.7455 0.99 2769 149 0.1488 0.2193 REMARK 3 4 2.7455 - 2.4945 0.97 2750 145 0.1462 0.2085 REMARK 3 5 2.4945 - 2.3158 0.97 2745 117 0.1449 0.1766 REMARK 3 6 2.3158 - 2.1792 0.96 2690 134 0.1483 0.2052 REMARK 3 7 2.1792 - 2.0701 0.95 2638 143 0.1621 0.2256 REMARK 3 8 2.0701 - 1.9800 0.94 2625 157 0.1690 0.2100 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 60.12 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.07250 REMARK 3 B22 (A**2) : -4.89100 REMARK 3 B33 (A**2) : 5.96350 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -6.35880 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 2203 REMARK 3 ANGLE : 1.212 2966 REMARK 3 CHIRALITY : 0.087 317 REMARK 3 PLANARITY : 0.005 371 REMARK 3 DIHEDRAL : 19.784 860 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 3:63) REMARK 3 ORIGIN FOR THE GROUP (A): -29.4606 -10.8542 10.1849 REMARK 3 T TENSOR REMARK 3 T11: 0.1079 T22: 0.2812 REMARK 3 T33: 0.1845 T12: -0.0168 REMARK 3 T13: -0.0551 T23: -0.0929 REMARK 3 L TENSOR REMARK 3 L11: 1.8964 L22: 1.0719 REMARK 3 L33: 1.6145 L12: -0.4079 REMARK 3 L13: 1.3599 L23: 0.2560 REMARK 3 S TENSOR REMARK 3 S11: 0.0589 S12: 0.6825 S13: -0.4494 REMARK 3 S21: -0.1658 S22: 0.0379 S23: 0.3849 REMARK 3 S31: 0.0500 S32: 0.1922 S33: -0.0523 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 64:157) REMARK 3 ORIGIN FOR THE GROUP (A): -18.1899 -3.5685 20.2085 REMARK 3 T TENSOR REMARK 3 T11: 0.0420 T22: 0.0880 REMARK 3 T33: 0.0378 T12: -0.0053 REMARK 3 T13: 0.0023 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 1.6984 L22: 1.1304 REMARK 3 L33: 0.0328 L12: 1.0032 REMARK 3 L13: 0.1542 L23: 0.0112 REMARK 3 S TENSOR REMARK 3 S11: -0.0113 S12: 0.1989 S13: 0.1334 REMARK 3 S21: -0.0364 S22: 0.0209 S23: 0.1336 REMARK 3 S31: 0.0430 S32: -0.0656 S33: 0.0021 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 158:279) REMARK 3 ORIGIN FOR THE GROUP (A): -6.0602 9.0524 19.3764 REMARK 3 T TENSOR REMARK 3 T11: 0.0547 T22: 0.0560 REMARK 3 T33: 0.0269 T12: -0.0074 REMARK 3 T13: 0.0068 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 0.9834 L22: 1.2230 REMARK 3 L33: 0.5304 L12: 0.5889 REMARK 3 L13: -0.2228 L23: 0.2581 REMARK 3 S TENSOR REMARK 3 S11: -0.0868 S12: 0.1713 S13: 0.0150 REMARK 3 S21: -0.0726 S22: 0.0519 S23: -0.0260 REMARK 3 S31: -0.0771 S32: -0.0708 S33: 0.0308 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 1280) REMARK 3 ORIGIN FOR THE GROUP (A): -26.4379 -2.4046 18.7578 REMARK 3 T TENSOR REMARK 3 T11: 0.1081 T22: 0.1657 REMARK 3 T33: 0.1712 T12: -0.0013 REMARK 3 T13: -0.0086 T23: 0.0510 REMARK 3 L TENSOR REMARK 3 L11: 1.8860 L22: 0.8693 REMARK 3 L33: 5.1072 L12: 0.5218 REMARK 3 L13: -2.1642 L23: -0.2244 REMARK 3 S TENSOR REMARK 3 S11: -0.2707 S12: 0.3876 S13: 0.3113 REMARK 3 S21: 0.0362 S22: 0.0819 S23: 0.0659 REMARK 3 S31: -0.0430 S32: -0.4241 S33: 0.1546 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2XNP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1290044973. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97630 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26646 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 46.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2W5A REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 50.82000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.44000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.82000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.44000 REMARK 290 SMTRY3 4 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2080 LIES ON A SPECIAL POSITION. 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 MET A 1 REMARK 465 PRO A 2 REMARK 465 SER A 18 REMARK 465 ASP A 132 REMARK 465 GLY A 133 REMARK 465 GLY A 134 REMARK 465 HIS A 135 REMARK 465 THR A 136 REMARK 465 VAL A 137 REMARK 465 LEU A 138 REMARK 465 ALA A 163 REMARK 465 ARG A 164 REMARK 465 ILE A 165 REMARK 465 LEU A 166 REMARK 465 ASN A 167 REMARK 465 HIS A 168 REMARK 465 ASP A 169 REMARK 465 THR A 170 REMARK 465 SER A 171 REMARK 465 PHE A 172 REMARK 465 ALA A 173 REMARK 465 LYS A 174 REMARK 465 THR A 175 REMARK 465 MET A 191 REMARK 465 SER A 192 REMARK 465 TYR A 193 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 ARG A 77 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 79 CG OD1 ND2 REMARK 470 ARG A 130 NE CZ NH1 NH2 REMARK 470 HIS A 139 CG ND1 CD2 CE1 NE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 54 CA REMARK 480 ARG A 69 CD NH2 REMARK 480 MET A 188 CG REMARK 480 GLN A 221 OE1 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 ASP A 76 79.12 -103.40 REMARK 500 THR A 80 52.00 38.21 REMARK 500 MET A 188 -19.30 -49.96 REMARK 500 ASN A 189 -28.00 -142.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2001 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A2002 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH A2017 DISTANCE = 6.74 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE WCX A 1280 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1282 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1288 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1283 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1284 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1285 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1286 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1289 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XKC RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO CCT241734 REMARK 900 RELATED ID: 2W5B RELATED DB: PDB REMARK 900 HUMAN NEK2 KINASE ATPGAMMAS-BOUND REMARK 900 RELATED ID: 2XK8 RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO CCT241799 REMARK 900 RELATED ID: 2WQO RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO THE AMINOPYRIDINE CCT241950 REMARK 900 RELATED ID: 2JAV RELATED DB: PDB REMARK 900 HUMAN KINASE WITH PYRROLE-INDOLINONE LIGAND REMARK 900 RELATED ID: 2XK6 RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO REMARK 900 RELATED ID: 2XK4 RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO CCT242101 REMARK 900 RELATED ID: 2XK3 RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO CCT244744 REMARK 900 RELATED ID: 2W5A RELATED DB: PDB REMARK 900 HUMAN NEK2 KINASE ADP-BOUND REMARK 900 RELATED ID: 2XKE RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO CCT193788 REMARK 900 RELATED ID: 2XK7 RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO CCT242010 REMARK 900 RELATED ID: 2W5H RELATED DB: PDB REMARK 900 HUMAN NEK2 KINASE APO REMARK 900 RELATED ID: 2XKD RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO CCT231393 REMARK 900 RELATED ID: 2XKF RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO CCT134934 REMARK 900 RELATED ID: 2XNN RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO CCT242430 REMARK 900 RELATED ID: 2XNM RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO CCT REMARK 900 RELATED ID: 2XNO RELATED DB: PDB REMARK 900 STRUCTURE OF NEK2 BOUND TO CCT243779 DBREF 2XNP A 1 271 UNP P51955 NEK2_HUMAN 1 271 SEQADV 2XNP LEU A 272 UNP P51955 EXPRESSION TAG SEQADV 2XNP GLU A 273 UNP P51955 EXPRESSION TAG SEQADV 2XNP HIS A 274 UNP P51955 EXPRESSION TAG SEQADV 2XNP HIS A 275 UNP P51955 EXPRESSION TAG SEQADV 2XNP HIS A 276 UNP P51955 EXPRESSION TAG SEQADV 2XNP HIS A 277 UNP P51955 EXPRESSION TAG SEQADV 2XNP HIS A 278 UNP P51955 EXPRESSION TAG SEQADV 2XNP HIS A 279 UNP P51955 EXPRESSION TAG SEQRES 1 A 279 MET PRO SER ARG ALA GLU ASP TYR GLU VAL LEU TYR THR SEQRES 2 A 279 ILE GLY THR GLY SER TYR GLY ARG CYS GLN LYS ILE ARG SEQRES 3 A 279 ARG LYS SER ASP GLY LYS ILE LEU VAL TRP LYS GLU LEU SEQRES 4 A 279 ASP TYR GLY SER MET THR GLU ALA GLU LYS GLN MET LEU SEQRES 5 A 279 VAL SER GLU VAL ASN LEU LEU ARG GLU LEU LYS HIS PRO SEQRES 6 A 279 ASN ILE VAL ARG TYR TYR ASP ARG ILE ILE ASP ARG THR SEQRES 7 A 279 ASN THR THR LEU TYR ILE VAL MET GLU TYR CYS GLU GLY SEQRES 8 A 279 GLY ASP LEU ALA SER VAL ILE THR LYS GLY THR LYS GLU SEQRES 9 A 279 ARG GLN TYR LEU ASP GLU GLU PHE VAL LEU ARG VAL MET SEQRES 10 A 279 THR GLN LEU THR LEU ALA LEU LYS GLU CYS HIS ARG ARG SEQRES 11 A 279 SER ASP GLY GLY HIS THR VAL LEU HIS ARG ASP LEU LYS SEQRES 12 A 279 PRO ALA ASN VAL PHE LEU ASP GLY LYS GLN ASN VAL LYS SEQRES 13 A 279 LEU GLY ASP PHE GLY LEU ALA ARG ILE LEU ASN HIS ASP SEQRES 14 A 279 THR SER PHE ALA LYS THR PHE VAL GLY THR PRO TYR TYR SEQRES 15 A 279 MET SER PRO GLU GLN MET ASN ARG MET SER TYR ASN GLU SEQRES 16 A 279 LYS SER ASP ILE TRP SER LEU GLY CYS LEU LEU TYR GLU SEQRES 17 A 279 LEU CYS ALA LEU MET PRO PRO PHE THR ALA PHE SER GLN SEQRES 18 A 279 LYS GLU LEU ALA GLY LYS ILE ARG GLU GLY LYS PHE ARG SEQRES 19 A 279 ARG ILE PRO TYR ARG TYR SER ASP GLU LEU ASN GLU ILE SEQRES 20 A 279 ILE THR ARG MET LEU ASN LEU LYS ASP TYR HIS ARG PRO SEQRES 21 A 279 SER VAL GLU GLU ILE LEU GLU ASN PRO LEU ILE LEU GLU SEQRES 22 A 279 HIS HIS HIS HIS HIS HIS HET WCX A1280 39 HET CL A1281 1 HET CL A1282 1 HET CL A1283 1 HET EDO A1284 4 HET EDO A1285 4 HET EDO A1286 4 HET EDO A1287 4 HET CL A1288 1 HET EDO A1289 4 HETNAM WCX 4-{5-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H-BENZIMIDAZOL-1- HETNAM 2 WCX YL}-2-{(1R)-1-[2-(TRIFLUOROMETHYL) HETNAM 3 WCX PHENYL]ETHOXY}BENZAMIDE HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 WCX C29 H29 F3 N4 O3 FORMUL 3 CL 4(CL 1-) FORMUL 6 EDO 5(C2 H6 O2) FORMUL 12 HOH *224(H2 O) HELIX 1 1 ARG A 4 GLU A 6 5 3 HELIX 2 2 THR A 45 GLU A 61 1 17 HELIX 3 3 LEU A 94 ARG A 105 1 12 HELIX 4 4 ASP A 109 SER A 131 1 23 HELIX 5 5 LYS A 143 ALA A 145 5 3 HELIX 6 6 ASN A 194 LEU A 212 1 19 HELIX 7 7 SER A 220 GLY A 231 1 12 HELIX 8 8 SER A 241 LEU A 252 1 12 HELIX 9 9 LYS A 255 ARG A 259 5 5 HELIX 10 10 SER A 261 GLU A 267 1 7 HELIX 11 11 LEU A 272 HIS A 276 5 5 SHEET 1 AA 5 TYR A 8 THR A 16 0 SHEET 2 AA 5 ARG A 21 ARG A 27 -1 O CYS A 22 N ILE A 14 SHEET 3 AA 5 ILE A 33 ASP A 40 -1 O LEU A 34 N ILE A 25 SHEET 4 AA 5 THR A 81 GLU A 87 -1 O LEU A 82 N LEU A 39 SHEET 5 AA 5 TYR A 70 ASP A 76 -1 N TYR A 71 O VAL A 85 SHEET 1 AB 3 GLY A 92 ASP A 93 0 SHEET 2 AB 3 VAL A 147 LEU A 149 -1 N LEU A 149 O GLY A 92 SHEET 3 AB 3 VAL A 155 LEU A 157 -1 O LYS A 156 N PHE A 148 SITE 1 AC1 16 ILE A 14 GLY A 15 TYR A 19 CYS A 22 SITE 2 AC1 16 GLU A 87 TYR A 88 CYS A 89 GLU A 90 SITE 3 AC1 16 GLY A 92 ASP A 93 ALA A 145 PHE A 148 SITE 4 AC1 16 GLY A 158 ASP A 159 PHE A 160 HOH A2216 SITE 1 AC2 4 ASN A 154 HIS A 277 HIS A 279 HOH A2132 SITE 1 AC3 1 HOH A2160 SITE 1 AC4 4 TYR A 207 PRO A 215 PHE A 233 ARG A 234 SITE 1 AC5 6 TYR A 181 TYR A 182 GLU A 208 PRO A 214 SITE 2 AC5 6 HOH A2217 HOH A2219 SITE 1 AC6 6 ASP A 242 GLU A 243 GLU A 246 HIS A 277 SITE 2 AC6 6 HIS A 279 HOH A2220 SITE 1 AC7 5 LYS A 152 GLN A 153 HOH A2131 HOH A2214 SITE 2 AC7 5 HOH A2221 SITE 1 AC8 6 GLU A 195 LYS A 196 SER A 261 VAL A 262 SITE 2 AC8 6 HOH A2117 HOH A2200 SITE 1 AC9 6 ARG A 234 ARG A 235 LEU A 266 HOH A2166 SITE 2 AC9 6 HOH A2222 HOH A2224 CRYST1 101.640 56.880 81.840 90.00 133.63 90.00 C 1 2 1 4 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 0.009839 0.000000 0.009379 0.00000 SCALE2 0.000000 0.017581 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016881 0.00000