HEADER TRANSFERASE/TRANSFERASE INHIBITOR 27-MAR-19 6JPJ TITLE CRYSTAL STRUCTURE OF FGF401 IN COMPLEX OF FGFR4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBROBLAST GROWTH FACTOR RECEPTOR 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FGFR-4; COMPND 5 EC: 2.7.10.1; COMPND 6 ENGINEERED: YES; COMPND 7 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: FGFR4, JTK2, TKF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FGF401, REVERSIBLE COVALENT INHIBITOR, FGFR4, TRANSFERASE-TRANSFERASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Z.ZHOU,X.CHEN,Y.CHEN REVDAT 4 16-OCT-24 6JPJ 1 REMARK REVDAT 3 22-NOV-23 6JPJ 1 REMARK HETSYN REVDAT 2 05-JUN-19 6JPJ 1 JRNL REVDAT 1 15-MAY-19 6JPJ 0 JRNL AUTH Z.ZHOU,X.CHEN,Y.FU,Y.ZHANG,S.DAI,J.LI,L.CHEN,G.XU,Z.CHEN, JRNL AUTH 2 Y.CHEN JRNL TITL CHARACTERIZATION OF FGF401 AS A REVERSIBLE COVALENT JRNL TITL 2 INHIBITOR OF FIBROBLAST GROWTH FACTOR RECEPTOR 4. JRNL REF CHEM.COMMUN.(CAMB.) V. 55 5890 2019 JRNL REFN ESSN 1364-548X JRNL PMID 31041948 JRNL DOI 10.1039/C9CC02052G REMARK 2 REMARK 2 RESOLUTION. 2.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 8713 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.290 REMARK 3 FREE R VALUE TEST SET COUNT : 461 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 41.8094 - 3.8033 1.00 2940 149 0.1626 0.1655 REMARK 3 2 3.8033 - 3.0191 1.00 2858 187 0.2093 0.3041 REMARK 3 3 3.0191 - 2.6375 0.85 2454 125 0.2670 0.3704 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.950 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 : 0.003 2462 REMARK 3 ANGLE : 0.675 3343 REMARK 3 CHIRALITY : 0.026 354 REMARK 3 PLANARITY : 0.002 434 REMARK 3 DIHEDRAL : 13.165 957 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 86.1129 7.4630 74.1564 REMARK 3 T TENSOR REMARK 3 T11: 0.2801 T22: 0.2807 REMARK 3 T33: 0.2565 T12: -0.0267 REMARK 3 T13: 0.0023 T23: -0.0072 REMARK 3 L TENSOR REMARK 3 L11: 0.6798 L22: 0.7132 REMARK 3 L33: 1.4659 L12: -0.1777 REMARK 3 L13: 0.5653 L23: -0.3144 REMARK 3 S TENSOR REMARK 3 S11: 0.0690 S12: 0.0261 S13: -0.0480 REMARK 3 S21: 0.0033 S22: -0.0880 S23: 0.0495 REMARK 3 S31: 0.1455 S32: 0.0458 S33: 0.0035 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 6JPJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-APR-19. REMARK 100 THE DEPOSITION ID IS D_1300011415. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8724 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.638 REMARK 200 RESOLUTION RANGE LOW (A) : 41.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 5JKG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES PH 5.5, 20% PEG 4000, 0.15M REMARK 280 (NH4)2SO4, 4% (V/V) FORMAMIDE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 30.46550 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: 390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 GLY A 443 REMARK 465 PRO A 444 REMARK 465 LEU A 445 REMARK 465 LEU A 446 REMARK 465 ALA A 447 REMARK 465 GLY A 448 REMARK 465 LEU A 449 REMARK 465 VAL A 450 REMARK 465 SER A 451 REMARK 465 LEU A 452 REMARK 465 ASP A 453 REMARK 465 GLU A 753 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 SER A 579 -1.89 -56.46 REMARK 500 HIS A 639 54.31 -144.39 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 FGF A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 802 DBREF 6JPJ A 445 753 UNP P22455 FGFR4_HUMAN 445 753 SEQADV 6JPJ GLY A 443 UNP P22455 EXPRESSION TAG SEQADV 6JPJ PRO A 444 UNP P22455 EXPRESSION TAG SEQADV 6JPJ ALA A 477 UNP P22455 CYS 477 ENGINEERED MUTATION SEQADV 6JPJ GLU A 664 UNP P22455 ARG 664 ENGINEERED MUTATION SEQRES 1 A 311 GLY PRO LEU LEU ALA GLY LEU VAL SER LEU ASP LEU PRO SEQRES 2 A 311 LEU ASP PRO LEU TRP GLU PHE PRO ARG ASP ARG LEU VAL SEQRES 3 A 311 LEU GLY LYS PRO LEU GLY GLU GLY ALA PHE GLY GLN VAL SEQRES 4 A 311 VAL ARG ALA GLU ALA PHE GLY MET ASP PRO ALA ARG PRO SEQRES 5 A 311 ASP GLN ALA SER THR VAL ALA VAL LYS MET LEU LYS ASP SEQRES 6 A 311 ASN ALA SER ASP LYS ASP LEU ALA ASP LEU VAL SER GLU SEQRES 7 A 311 MET GLU VAL MET LYS LEU ILE GLY ARG HIS LYS ASN ILE SEQRES 8 A 311 ILE ASN LEU LEU GLY VAL CYS THR GLN GLU GLY PRO LEU SEQRES 9 A 311 TYR VAL ILE VAL GLU CYS ALA ALA LYS GLY ASN LEU ARG SEQRES 10 A 311 GLU PHE LEU ARG ALA ARG ARG PRO PRO GLY PRO ASP LEU SEQRES 11 A 311 SER PRO ASP GLY PRO ARG SER SER GLU GLY PRO LEU SER SEQRES 12 A 311 PHE PRO VAL LEU VAL SER CYS ALA TYR GLN VAL ALA ARG SEQRES 13 A 311 GLY MET GLN TYR LEU GLU SER ARG LYS CYS ILE HIS ARG SEQRES 14 A 311 ASP LEU ALA ALA ARG ASN VAL LEU VAL THR GLU ASP ASN SEQRES 15 A 311 VAL MET LYS ILE ALA ASP PHE GLY LEU ALA ARG GLY VAL SEQRES 16 A 311 HIS HIS ILE ASP TYR TYR LYS LYS THR SER ASN GLY ARG SEQRES 17 A 311 LEU PRO VAL LYS TRP MET ALA PRO GLU ALA LEU PHE ASP SEQRES 18 A 311 GLU VAL TYR THR HIS GLN SER ASP VAL TRP SER PHE GLY SEQRES 19 A 311 ILE LEU LEU TRP GLU ILE PHE THR LEU GLY GLY SER PRO SEQRES 20 A 311 TYR PRO GLY ILE PRO VAL GLU GLU LEU PHE SER LEU LEU SEQRES 21 A 311 ARG GLU GLY HIS ARG MET ASP ARG PRO PRO HIS CYS PRO SEQRES 22 A 311 PRO GLU LEU TYR GLY LEU MET ARG GLU CYS TRP HIS ALA SEQRES 23 A 311 ALA PRO SER GLN ARG PRO THR PHE LYS GLN LEU VAL GLU SEQRES 24 A 311 ALA LEU ASP LYS VAL LEU LEU ALA VAL SER GLU GLU HET FGF A 800 37 HET SO4 A 801 5 HET SO4 A 802 5 HETNAM FGF N-[5-CYANO-4-(2-METHOXYETHYLAMINO)PYRIDIN-2-YL]-7- HETNAM 2 FGF METHANOYL-6-[(4-METHYL-2-OXIDANYLIDENE-PIPERAZIN-1- HETNAM 3 FGF YL)METHYL]-3,4-DIHYDRO-2H-1,8-NAPHTHYRIDINE-1- HETNAM 4 FGF CARBOXAMIDE HETNAM SO4 SULFATE ION HETSYN FGF ROBLITINIB; FGF-401 FORMUL 2 FGF C25 H30 N8 O4 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *45(H2 O) HELIX 1 AA1 PRO A 463 ASP A 465 5 3 HELIX 2 AA2 SER A 510 GLY A 528 1 19 HELIX 3 AA3 ASN A 557 ALA A 564 1 8 HELIX 4 AA4 SER A 585 ARG A 606 1 22 HELIX 5 AA5 ALA A 614 ARG A 616 5 3 HELIX 6 AA6 GLY A 636 ILE A 640 5 5 HELIX 7 AA7 LEU A 651 MET A 656 5 6 HELIX 8 AA8 ALA A 657 PHE A 662 1 6 HELIX 9 AA9 THR A 667 PHE A 683 1 17 HELIX 10 AB1 PRO A 694 GLY A 705 1 12 HELIX 11 AB2 PRO A 715 TRP A 726 1 12 HELIX 12 AB3 ALA A 729 ARG A 733 5 5 HELIX 13 AB4 THR A 735 VAL A 750 1 16 SHEET 1 AA1 5 LEU A 467 GLY A 476 0 SHEET 2 AA1 5 GLY A 479 PHE A 487 -1 O GLY A 479 N GLY A 476 SHEET 3 AA1 5 ALA A 497 MET A 504 -1 O VAL A 502 N VAL A 482 SHEET 4 AA1 5 TYR A 547 VAL A 550 -1 O VAL A 548 N LYS A 503 SHEET 5 AA1 5 LEU A 536 CYS A 540 -1 N CYS A 540 O TYR A 547 SHEET 1 AA2 2 VAL A 618 VAL A 620 0 SHEET 2 AA2 2 MET A 626 ILE A 628 -1 O LYS A 627 N LEU A 619 LINK SG CYS A 552 CAL FGF A 800 1555 1555 1.77 SITE 1 AC1 12 LEU A 473 VAL A 481 ARG A 483 THR A 499 SITE 2 AC1 12 VAL A 500 ALA A 501 LYS A 503 GLU A 551 SITE 3 AC1 12 CYS A 552 ALA A 553 ALA A 554 LEU A 619 SITE 1 AC2 5 ARG A 616 THR A 646 ASN A 648 ARG A 650 SITE 2 AC2 5 HOH A 917 SITE 1 AC3 4 ARG A 563 ARG A 566 GLY A 687 HOH A 907 CRYST1 42.275 60.931 61.154 90.00 98.56 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 0.023655 0.000000 0.003560 0.00000 SCALE2 0.000000 0.016412 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016536 0.00000