HEADER CELL ADHESION 19-APR-18 6GCR TITLE FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH IRREVERSIBLE TITLE 2 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: FOCAL ADHESION KINASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FADK 1,FOCAL ADHESION KINASE-RELATED NONKINASE,P41/P43FRNK, COMPND 5 PROTEIN-TYROSINE KINASE 2,P125FAK,PP125FAK; COMPND 6 EC: 2.7.10.2; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 GENE: PTK2, FAK, FAK1; SOURCE 6 EXPRESSION_SYSTEM: UNIDENTIFIED BACULOVIRUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10469 KEYWDS FOCAL ADHESION KINASE CELL ADHESION SIGNALLING IRREVERSIBLE INHIBITOR KEYWDS 2 2, 4-PYRIMIDINE DERIVATIVES, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR E.YEN-PON,B.LI,M.ACEBRON-GARCIA DE EULATE,C.TOMKIEWICZ-RAULET, AUTHOR 2 J.DAWSON,D.LIETHA,M.C.FRAME,X.COUMOUL,C.GARBAY,M.ETHEVE-QUELQUEJEU, AUTHOR 3 H.CHEN REVDAT 2 02-OCT-19 6GCR 1 JRNL REVDAT 1 01-MAY-19 6GCR 0 JRNL AUTH E.YEN-PON,B.LI,M.ACEBRON-GARCIA-DE-EULATE, JRNL AUTH 2 C.TOMKIEWICZ-RAULET,J.DAWSON,D.LIETHA,M.C.FRAME,X.COUMOUL, JRNL AUTH 3 C.GARBAY,M.ETHEVE-QUELQUEJEU,H.CHEN JRNL TITL STRUCTURE-BASED DESIGN, SYNTHESIS, AND CHARACTERIZATION OF JRNL TITL 2 THE FIRST IRREVERSIBLE INHIBITOR OF FOCAL ADHESION KINASE. JRNL REF ACS CHEM.BIOL. V. 13 2067 2018 JRNL REFN ESSN 1554-8937 JRNL PMID 29897729 JRNL DOI 10.1021/ACSCHEMBIO.8B00250 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 11701 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.310 REMARK 3 FREE R VALUE TEST SET COUNT : 621 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 45.9348 - 3.6506 0.95 2813 149 0.1717 0.2147 REMARK 3 2 3.6506 - 2.8977 0.94 2727 145 0.2310 0.3015 REMARK 3 3 2.8977 - 2.5315 0.95 2730 165 0.2732 0.3718 REMARK 3 4 2.5315 - 2.3000 0.99 2810 162 0.2626 0.3126 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 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 : 0.009 2158 REMARK 3 ANGLE : 1.061 2917 REMARK 3 CHIRALITY : 0.055 316 REMARK 3 PLANARITY : 0.006 370 REMARK 3 DIHEDRAL : 7.076 1329 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6GCR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200008723. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18111 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 45.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.57400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: REMARK 280 T REMARK 280 RDYEIQRERIELGRCIGEGQFGDVHQGIYMSPENPALAVAIKTCKNCTSDSVREKFLQEALTMRQ REMARK 280 FDHPHIVKLIGVI TENPVWIIMELCTLGELRSFLQVRKYSLDLASLILYAYQLSTALAYLESKR REMARK 280 FVHRDIAARNVLVSSNDCVKLGDFGLSRY MEDSTYYKASKGKLPIKWMAPESINFRRFTSASDV REMARK 280 WMFGVCMWEILMHGVKPFQGVKNNDVIGRIENGERLPMPPNCPPT LYSLMTKCWAYDPSRRPRF REMARK 280 TELKAQLSTILEEEKLQ, PH 8.5, EVAPORATION, TEMPERATURE 291.1K 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 22.45000 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 SER A 411 REMARK 465 THR A 412 REMARK 465 TYR A 570 REMARK 465 MET A 571 REMARK 465 GLU A 572 REMARK 465 ASP A 573 REMARK 465 SER A 574 REMARK 465 THR A 575 REMARK 465 TYR A 576 REMARK 465 TYR A 577 REMARK 465 LYS A 578 REMARK 465 ALA A 579 REMARK 465 SER A 580 REMARK 465 LYS A 581 REMARK 465 GLY A 582 REMARK 465 LYS A 583 REMARK 465 LEU A 685 REMARK 465 GLN A 686 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 ASN A 458 CG OD1 ND2 REMARK 470 ARG A 597 CG CD NE CZ NH1 NH2 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 PHE A 516 0.07 -67.68 REMARK 500 ARG A 545 -5.76 81.04 REMARK 500 ASP A 546 51.53 -144.92 REMARK 500 ALA A 548 145.73 -177.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EUW A 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6GCX RELATED DB: PDB REMARK 900 RELATED ID: 6GCW RELATED DB: PDB DBREF 6GCR A 411 686 UNP Q00944 FAK1_CHICK 411 686 SEQRES 1 A 276 SER THR ARG ASP TYR GLU ILE GLN ARG GLU ARG ILE GLU SEQRES 2 A 276 LEU GLY ARG CYS ILE GLY GLU GLY GLN PHE GLY ASP VAL SEQRES 3 A 276 HIS GLN GLY ILE TYR MET SER PRO GLU ASN PRO ALA MET SEQRES 4 A 276 ALA VAL ALA ILE LYS THR CYS LYS ASN CYS THR SER ASP SEQRES 5 A 276 SER VAL ARG GLU LYS PHE LEU GLN GLU ALA LEU THR MET SEQRES 6 A 276 ARG GLN PHE ASP HIS PRO HIS ILE VAL LYS LEU ILE GLY SEQRES 7 A 276 VAL ILE THR GLU ASN PRO VAL TRP ILE ILE MET GLU LEU SEQRES 8 A 276 CYS THR LEU GLY GLU LEU ARG SER PHE LEU GLN VAL ARG SEQRES 9 A 276 LYS PHE SER LEU ASP LEU ALA SER LEU ILE LEU TYR ALA SEQRES 10 A 276 TYR GLN LEU SER THR ALA LEU ALA TYR LEU GLU SER LYS SEQRES 11 A 276 ARG PHE VAL HIS ARG ASP ILE ALA ALA ARG ASN VAL LEU SEQRES 12 A 276 VAL SER ALA THR ASP CYS VAL LYS LEU GLY ASP PHE GLY SEQRES 13 A 276 LEU SER ARG TYR MET GLU ASP SER THR TYR TYR LYS ALA SEQRES 14 A 276 SER LYS GLY LYS LEU PRO ILE LYS TRP MET ALA PRO GLU SEQRES 15 A 276 SER ILE ASN PHE ARG ARG PHE THR SER ALA SER ASP VAL SEQRES 16 A 276 TRP MET PHE GLY VAL CYS MET TRP GLU ILE LEU MET HIS SEQRES 17 A 276 GLY VAL LYS PRO PHE GLN GLY VAL LYS ASN ASN ASP VAL SEQRES 18 A 276 ILE GLY ARG ILE GLU ASN GLY GLU ARG LEU PRO MET PRO SEQRES 19 A 276 PRO ASN CYS PRO PRO THR LEU TYR SER LEU MET THR LYS SEQRES 20 A 276 CYS TRP ALA TYR ASP PRO SER ARG ARG PRO ARG PHE THR SEQRES 21 A 276 GLU LEU LYS ALA GLN LEU SER THR ILE LEU GLU GLU GLU SEQRES 22 A 276 LYS LEU GLN HET EUW A 701 41 HETNAM EUW 2-[[2-[[4-[[[3,4-BIS(OXIDANYLIDENE)-2-[2- HETNAM 2 EUW (PROPANOYLAMINO)ETHYLAMINO]CYCLOBUTEN-1- HETNAM 3 EUW YL]AMINO]METHYL]PHENYL]AMINO]-5-CHLORANYL-PYRIMIDIN-4- HETNAM 4 EUW YL]AMINO]-~{N}-METHYL-BENZAMIDE FORMUL 2 EUW C28 H29 CL N8 O4 FORMUL 3 HOH *66(H2 O) HELIX 1 AA1 GLN A 418 GLU A 420 5 3 HELIX 2 AA2 SER A 461 GLN A 477 1 17 HELIX 3 AA3 LEU A 507 ARG A 514 1 8 HELIX 4 AA4 LYS A 515 LEU A 518 5 4 HELIX 5 AA5 ASP A 519 LYS A 540 1 22 HELIX 6 AA6 ALA A 548 ARG A 550 5 3 HELIX 7 AA7 PRO A 585 MET A 589 5 5 HELIX 8 AA8 ALA A 590 ARG A 597 1 8 HELIX 9 AA9 THR A 600 MET A 617 1 18 HELIX 10 AB1 LYS A 627 GLY A 638 1 12 HELIX 11 AB2 PRO A 648 TRP A 659 1 12 HELIX 12 AB3 ASP A 662 ARG A 666 5 5 HELIX 13 AB4 ARG A 668 LYS A 684 1 17 SHEET 1 AA1 5 ILE A 422 GLY A 431 0 SHEET 2 AA1 5 GLY A 434 SER A 443 -1 O VAL A 436 N ILE A 428 SHEET 3 AA1 5 ASN A 446 THR A 455 -1 O ILE A 453 N HIS A 437 SHEET 4 AA1 5 TRP A 496 GLU A 500 -1 O MET A 499 N ALA A 452 SHEET 5 AA1 5 LEU A 486 ILE A 490 -1 N ILE A 487 O ILE A 498 SHEET 1 AA2 3 GLY A 505 GLU A 506 0 SHEET 2 AA2 3 VAL A 552 ALA A 556 -1 O VAL A 554 N GLY A 505 SHEET 3 AA2 3 CYS A 559 LEU A 562 -1 O LYS A 561 N LEU A 553 LINK SG CYS A 427 CBB EUW A 701 1555 1555 1.77 CISPEP 1 ASN A 493 PRO A 494 0 -4.03 SITE 1 AC1 14 ARG A 426 CYS A 427 ILE A 428 GLY A 429 SITE 2 AC1 14 GLU A 500 LEU A 501 CYS A 502 GLY A 505 SITE 3 AC1 14 GLU A 506 ASN A 551 LEU A 553 ASP A 564 SITE 4 AC1 14 LEU A 567 SER A 568 CRYST1 46.088 44.900 66.400 90.00 94.81 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 0.021698 0.000000 0.001826 0.00000 SCALE2 0.000000 0.022272 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015113 0.00000