HEADER TRANSFERASE/INHIBITOR 21-AUG-23 8KH9 TITLE CRYSTAL STRUCTURE OF FGFR4(V550M) KINASE DOMAIN WITH 8Z COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBROBLAST GROWTH FACTOR RECEPTOR 4; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 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; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, FGFR4, TRANSFERASE, TRANSFERASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Q.M.LIN,X.J.CHEN,Y.H.CHEN REVDAT 1 31-JUL-24 8KH9 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. 1.42 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 58191 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 2868 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 36.8800 - 3.8500 1.00 2820 154 0.1582 0.1544 REMARK 3 2 3.8500 - 3.0600 1.00 2824 138 0.1490 0.1600 REMARK 3 3 3.0600 - 2.6700 1.00 2781 136 0.1696 0.2034 REMARK 3 4 2.6700 - 2.4300 1.00 2794 141 0.1683 0.1978 REMARK 3 5 2.4300 - 2.2500 1.00 2761 161 0.1604 0.1754 REMARK 3 6 2.2500 - 2.1200 1.00 2780 129 0.1607 0.1971 REMARK 3 7 2.1200 - 2.0100 1.00 2729 167 0.1556 0.1889 REMARK 3 8 2.0100 - 1.9300 1.00 2772 158 0.1669 0.2079 REMARK 3 9 1.9300 - 1.8500 1.00 2776 145 0.1726 0.1914 REMARK 3 10 1.8500 - 1.7900 1.00 2758 146 0.1699 0.2054 REMARK 3 11 1.7900 - 1.7300 1.00 2777 139 0.1662 0.2036 REMARK 3 12 1.7300 - 1.6800 1.00 2755 148 0.1727 0.2287 REMARK 3 13 1.6800 - 1.6400 1.00 2726 153 0.1843 0.2313 REMARK 3 14 1.6400 - 1.6000 1.00 2789 142 0.1898 0.2281 REMARK 3 15 1.6000 - 1.5600 1.00 2730 136 0.2007 0.2015 REMARK 3 16 1.5600 - 1.5300 1.00 2787 128 0.2165 0.2512 REMARK 3 17 1.5300 - 1.5000 1.00 2750 141 0.2173 0.2292 REMARK 3 18 1.5000 - 1.4700 1.00 2762 113 0.2175 0.2807 REMARK 3 19 1.4700 - 1.4400 0.99 2742 132 0.2412 0.2330 REMARK 3 20 1.4400 - 1.4200 0.98 2710 161 0.2738 0.3179 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) : 19.450 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 2449 REMARK 3 ANGLE : 1.083 3329 REMARK 3 CHIRALITY : 0.095 354 REMARK 3 PLANARITY : 0.012 432 REMARK 3 DIHEDRAL : 16.386 345 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 8KH9 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_1300039122. 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) : 0.97918 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58347 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 61.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 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: 7WCX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS (PH 4.5), 0.2 M LI2SO4, REMARK 280 16-19 % PEG 3350, 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 30.80250 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 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 ASP A 571 CG OD1 OD2 REMARK 470 LYS A 607 CG CD CE NZ REMARK 470 LYS A 644 CG CD CE NZ REMARK 470 GLU A 752 CG CD OE1 OE2 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 -10.33 82.55 REMARK 500 ASP A 612 52.17 -146.06 REMARK 500 HIS A 639 52.05 -146.33 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 A1350 DISTANCE = 5.84 ANGSTROMS DBREF 8KH9 A 454 753 UNP P22455 FGFR4_HUMAN 454 753 SEQADV 8KH9 ALA A 477 UNP P22455 CYS 477 ENGINEERED MUTATION SEQADV 8KH9 MET A 550 UNP P22455 VAL 550 ENGINEERED MUTATION SEQADV 8KH9 GLU A 664 UNP P22455 ARG 664 ENGINEERED MUTATION SEQRES 1 A 300 LEU PRO LEU ASP PRO LEU TRP GLU PHE PRO ARG ASP ARG SEQRES 2 A 300 LEU VAL LEU GLY LYS PRO LEU GLY GLU GLY ALA PHE GLY SEQRES 3 A 300 GLN VAL VAL ARG ALA GLU ALA PHE GLY MET ASP PRO ALA SEQRES 4 A 300 ARG PRO ASP GLN ALA SER THR VAL ALA VAL LYS MET LEU SEQRES 5 A 300 LYS ASP ASN ALA SER ASP LYS ASP LEU ALA ASP LEU VAL SEQRES 6 A 300 SER GLU MET GLU VAL MET LYS LEU ILE GLY ARG HIS LYS SEQRES 7 A 300 ASN ILE ILE ASN LEU LEU GLY VAL CYS THR GLN GLU GLY SEQRES 8 A 300 PRO LEU TYR VAL ILE MET GLU CYS ALA ALA LYS GLY ASN SEQRES 9 A 300 LEU ARG GLU PHE LEU ARG ALA ARG ARG PRO PRO GLY PRO SEQRES 10 A 300 ASP LEU SER PRO ASP GLY PRO ARG SER SER GLU GLY PRO SEQRES 11 A 300 LEU SER PHE PRO VAL LEU VAL SER CYS ALA TYR GLN VAL SEQRES 12 A 300 ALA ARG GLY MET GLN TYR LEU GLU SER ARG LYS CYS ILE SEQRES 13 A 300 HIS ARG ASP LEU ALA ALA ARG ASN VAL LEU VAL THR GLU SEQRES 14 A 300 ASP ASN VAL MET LYS ILE ALA ASP PHE GLY LEU ALA ARG SEQRES 15 A 300 GLY VAL HIS HIS ILE ASP TYR TYR LYS LYS THR SER ASN SEQRES 16 A 300 GLY ARG LEU PRO VAL LYS TRP MET ALA PRO GLU ALA LEU SEQRES 17 A 300 PHE ASP GLU VAL TYR THR HIS GLN SER ASP VAL TRP SER SEQRES 18 A 300 PHE GLY ILE LEU LEU TRP GLU ILE PHE THR LEU GLY GLY SEQRES 19 A 300 SER PRO TYR PRO GLY ILE PRO VAL GLU GLU LEU PHE SER SEQRES 20 A 300 LEU LEU ARG GLU GLY HIS ARG MET ASP ARG PRO PRO HIS SEQRES 21 A 300 CYS PRO PRO GLU LEU TYR GLY LEU MET ARG GLU CYS TRP SEQRES 22 A 300 HIS ALA ALA PRO SER GLN ARG PRO THR PHE LYS GLN LEU SEQRES 23 A 300 VAL GLU ALA LEU ASP LYS VAL LEU LEU ALA VAL SER GLU SEQRES 24 A 300 GLU HET EDO A 901 4 HET SO4 A 902 5 HET VVW A 903 49 HETNAM EDO 1,2-ETHANEDIOL 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 HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 SO4 O4 S 2- FORMUL 4 VVW C32 H35 CL2 N9 O6 FORMUL 5 HOH *350(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 MET 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 903 1555 1555 1.70 CRYST1 42.398 61.605 60.605 90.00 97.93 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 0.023586 0.000000 0.003285 0.00000 SCALE2 0.000000 0.016233 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016659 0.00000