HEADER TRANSFERASE/INHIBITOR 21-AUG-23 8KH8 TITLE CRYSTAL STRUCTURE OF FGFR4(V550L) KINASE DOMAIN WITH 8Z 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 FGFR4 KINASE DOMAIN, TRANSFERASE, TRANSFERASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Q.M.LIN,X.J.CHEN,Y.H.CHEN REVDAT 1 31-JUL-24 8KH8 0 JRNL AUTH F.YANG,Q.LIN,X.SONG,H.HUANG,X.CHEN,J.TAN,Y.LI,Y.ZHOU,Z.TU, JRNL AUTH 2 H.DU,Z.M.ZHANG,R.ORTEGA,X.LIN,A.V.PATTERSON,J.B.SMAILL, JRNL AUTH 3 Y.CHEN,X.LU JRNL TITL DISCOVERY OF 6-FORMYLPYRIDYL UREA DERIVATIVES AS POTENT JRNL TITL 2 REVERSIBLE-COVALENT FIBROBLAST GROWTH FACTOR RECEPTOR 4 JRNL TITL 3 INHIBITORS WITH IMPROVED ANTI-HEPATOCELLULAR CARCINOMA JRNL TITL 4 ACTIVITY. JRNL REF J.MED.CHEM. V. 67 2667 2024 JRNL REFN ISSN 0022-2623 JRNL PMID 38348819 JRNL DOI 10.1021/ACS.JMEDCHEM.3C01810 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) 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) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 49829 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 2537 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 36.6600 - 3.9000 1.00 2688 158 0.1593 0.1335 REMARK 3 2 3.9000 - 3.1000 1.00 2696 112 0.1458 0.1966 REMARK 3 3 3.1000 - 2.7100 1.00 2641 146 0.1625 0.1939 REMARK 3 4 2.7100 - 2.4600 1.00 2633 151 0.1692 0.2025 REMARK 3 5 2.4600 - 2.2800 1.00 2650 128 0.1627 0.1654 REMARK 3 6 2.2800 - 2.1500 1.00 2627 139 0.1566 0.2128 REMARK 3 7 2.1500 - 2.0400 1.00 2665 124 0.1556 0.2009 REMARK 3 8 2.0400 - 1.9500 1.00 2601 146 0.1633 0.2149 REMARK 3 9 1.9500 - 1.8800 1.00 2603 165 0.1738 0.2035 REMARK 3 10 1.8800 - 1.8100 1.00 2626 150 0.1705 0.2388 REMARK 3 11 1.8100 - 1.7600 1.00 2607 134 0.1701 0.2236 REMARK 3 12 1.7600 - 1.7100 1.00 2661 125 0.1761 0.2038 REMARK 3 13 1.7100 - 1.6600 1.00 2598 149 0.1843 0.2294 REMARK 3 14 1.6600 - 1.6200 1.00 2584 153 0.1951 0.2279 REMARK 3 15 1.6200 - 1.5800 1.00 2634 141 0.2027 0.2369 REMARK 3 16 1.5800 - 1.5500 0.99 2589 151 0.2158 0.2435 REMARK 3 17 1.5500 - 1.5200 0.99 2611 128 0.2225 0.2706 REMARK 3 18 1.5200 - 1.4900 0.99 2578 137 0.2389 0.2682 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.920 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 : 0.008 2451 REMARK 3 ANGLE : 1.035 3333 REMARK 3 CHIRALITY : 0.095 355 REMARK 3 PLANARITY : 0.012 433 REMARK 3 DIHEDRAL : 17.494 345 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 8KH8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1300039142. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-23 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49894 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 61.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHENIX REMARK 200 STARTING MODEL: 7WCW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS (PH 4.5), 0.2 M LI2SO4, REMARK 280 16-19% PEG3350, VAPOR DIFFUSION, HANGING DROP, 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 30.72850 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 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 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 GLU A 752 REMARK 465 GLU A 753 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 471 CG CD CE NZ REMARK 470 ARG A 529 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 607 CG CD CE NZ REMARK 470 GLU A 622 CG CD OE1 OE2 REMARK 470 LYS A 644 CG CD CE NZ 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 611 -11.36 83.49 REMARK 500 ASP A 612 52.50 -145.88 REMARK 500 HIS A 639 54.38 -144.22 REMARK 500 REMARK 500 REMARK: NULL DBREF 8KH8 A 445 753 UNP P22455 FGFR4_HUMAN 445 753 SEQADV 8KH8 ALA A 477 UNP P22455 CYS 477 ENGINEERED MUTATION SEQADV 8KH8 LEU A 550 UNP P22455 VAL 550 ENGINEERED MUTATION SEQADV 8KH8 GLU A 664 UNP P22455 ARG 664 ENGINEERED MUTATION SEQRES 1 A 309 LEU LEU ALA GLY LEU VAL SER LEU ASP LEU PRO LEU ASP SEQRES 2 A 309 PRO LEU TRP GLU PHE PRO ARG ASP ARG LEU VAL LEU GLY SEQRES 3 A 309 LYS PRO LEU GLY GLU GLY ALA PHE GLY GLN VAL VAL ARG SEQRES 4 A 309 ALA GLU ALA PHE GLY MET ASP PRO ALA ARG PRO ASP GLN SEQRES 5 A 309 ALA SER THR VAL ALA VAL LYS MET LEU LYS ASP ASN ALA SEQRES 6 A 309 SER ASP LYS ASP LEU ALA ASP LEU VAL SER GLU MET GLU SEQRES 7 A 309 VAL MET LYS LEU ILE GLY ARG HIS LYS ASN ILE ILE ASN SEQRES 8 A 309 LEU LEU GLY VAL CYS THR GLN GLU GLY PRO LEU TYR VAL SEQRES 9 A 309 ILE LEU GLU CYS ALA ALA LYS GLY ASN LEU ARG GLU PHE SEQRES 10 A 309 LEU ARG ALA ARG ARG PRO PRO GLY PRO ASP LEU SER PRO SEQRES 11 A 309 ASP GLY PRO ARG SER SER GLU GLY PRO LEU SER PHE PRO SEQRES 12 A 309 VAL LEU VAL SER CYS ALA TYR GLN VAL ALA ARG GLY MET SEQRES 13 A 309 GLN TYR LEU GLU SER ARG LYS CYS ILE HIS ARG ASP LEU SEQRES 14 A 309 ALA ALA ARG ASN VAL LEU VAL THR GLU ASP ASN VAL MET SEQRES 15 A 309 LYS ILE ALA ASP PHE GLY LEU ALA ARG GLY VAL HIS HIS SEQRES 16 A 309 ILE ASP TYR TYR LYS LYS THR SER ASN GLY ARG LEU PRO SEQRES 17 A 309 VAL LYS TRP MET ALA PRO GLU ALA LEU PHE ASP GLU VAL SEQRES 18 A 309 TYR THR HIS GLN SER ASP VAL TRP SER PHE GLY ILE LEU SEQRES 19 A 309 LEU TRP GLU ILE PHE THR LEU GLY GLY SER PRO TYR PRO SEQRES 20 A 309 GLY ILE PRO VAL GLU GLU LEU PHE SER LEU LEU ARG GLU SEQRES 21 A 309 GLY HIS ARG MET ASP ARG PRO PRO HIS CYS PRO PRO GLU SEQRES 22 A 309 LEU TYR GLY LEU MET ARG GLU CYS TRP HIS ALA ALA PRO SEQRES 23 A 309 SER GLN ARG PRO THR PHE LYS GLN LEU VAL GLU ALA LEU SEQRES 24 A 309 ASP LYS VAL LEU LEU ALA VAL SER GLU GLU HET SO4 A 801 5 HET VVW A 802 49 HET EDO A 803 4 HETNAM SO4 SULFATE ION HETNAM VVW 1-[4-[(1~{R})-1-[3,5-BIS(CHLORANYL)PYRIDIN-4- HETNAM 2 VVW YL]ETHOXY]-5-CYANO-PYRIDIN-2-YL]-3-[6-METHANOYL-5-[(4- HETNAM 3 VVW METHYL-2-OXIDANYLIDENE-PIPERAZIN-1-YL)METHYL]-3-(2- HETNAM 4 VVW MORPHOLIN-4-YLETHOXY)PYRIDIN-2-YL]UREA HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 SO4 O4 S 2- FORMUL 3 VVW C32 H35 CL2 N9 O6 FORMUL 4 EDO C2 H6 O2 FORMUL 5 HOH *340(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 LEU A 651 MET A 656 5 6 HELIX 7 AA7 ALA A 657 GLU A 664 1 8 HELIX 8 AA8 THR A 667 THR A 684 1 18 HELIX 9 AA9 PRO A 694 GLU A 704 1 11 HELIX 10 AB1 PRO A 715 TRP A 726 1 12 HELIX 11 AB2 ALA A 729 ARG A 733 5 5 HELIX 12 AB3 THR A 735 SER A 751 1 17 SHEET 1 AA1 5 LEU A 467 GLU A 475 0 SHEET 2 AA1 5 GLN A 480 PHE A 487 -1 O ARG A 483 N GLY A 470 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 GLU A 551 -1 O LEU A 550 N ALA A 501 SHEET 5 AA1 5 LEU A 536 CYS A 540 -1 N LEU A 537 O ILE A 549 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 C3 VVW A 802 1555 1555 1.76 CRYST1 42.141 61.457 60.417 90.00 97.82 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 0.023730 0.000000 0.003261 0.00000 SCALE2 0.000000 0.016272 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016707 0.00000