HEADER TRANSFERASE/INHIBITOR 29-JUN-22 7YBO TITLE CRYSTAL STRUCTURE OF FGFR4 KINASE DOMAIN WITH 10Z COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBROBLAST GROWTH FACTOR RECEPTOR 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN; COMPND 5 SYNONYM: FGFR-4; COMPND 6 EC: 2.7.10.1; COMPND 7 ENGINEERED: YES; COMPND 8 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 KINASE, INHIBITOR, STRUCTURAL PROTEIN, TRANSFERASE-TRANSFERASE KEYWDS 2 INHIBITOR COMPLEX, TRANSFERASE, TRANSFERASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.J.CHEN,Q.M.LIN,Y.H.CHEN REVDAT 3 29-NOV-23 7YBO 1 REMARK REVDAT 2 23-NOV-22 7YBO 1 JRNL REVDAT 1 16-NOV-22 7YBO 0 JRNL AUTH F.YANG,X.CHEN,X.SONG,R.ORTEGA,X.LIN,W.DENG,J.GUO,Z.TU, JRNL AUTH 2 A.V.PATTERSON,J.B.SMAILL,Y.CHEN,X.LU JRNL TITL DESIGN, SYNTHESIS, AND BIOLOGICAL EVALUATION OF JRNL TITL 2 5-FORMYL-PYRROLO[3,2- B ]PYRIDINE-3-CARBOXAMIDES AS NEW JRNL TITL 3 SELECTIVE, POTENT, AND REVERSIBLE-COVALENT FGFR4 INHIBITORS. JRNL REF J.MED.CHEM. V. 65 14809 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 36278929 JRNL DOI 10.1021/ACS.JMEDCHEM.2C01319 REMARK 2 REMARK 2 RESOLUTION. 2.31 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 11872 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.690 REMARK 3 FREE R VALUE TEST SET COUNT : 557 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 42.4650 - 3.6609 1.00 3065 149 0.1777 0.2122 REMARK 3 2 3.6609 - 2.9059 1.00 3011 155 0.2211 0.2772 REMARK 3 3 2.9059 - 2.5387 0.99 2962 162 0.2466 0.3063 REMARK 3 4 2.5387 - 2.3070 0.76 2277 91 0.2497 0.3146 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.08 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 2437 REMARK 3 ANGLE : 0.776 3312 REMARK 3 CHIRALITY : 0.029 350 REMARK 3 PLANARITY : 0.003 424 REMARK 3 DIHEDRAL : 14.253 920 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 7YBO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300030621. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 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) : 1.5870 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11880 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.307 REMARK 200 RESOLUTION RANGE LOW (A) : 42.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.17290 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.28790 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 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: 7WCT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 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 30.22000 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 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 CYS A 477 REMARK 465 GLY A 569 REMARK 465 PRO A 570 REMARK 465 ASP A 571 REMARK 465 LEU A 572 REMARK 465 SER A 573 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 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 -3.15 72.25 REMARK 500 ASP A 612 26.94 -146.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 7YBO A 445 753 UNP P22455 FGFR4_HUMAN 445 753 SEQADV 7YBO GLY A 443 UNP P22455 EXPRESSION TAG SEQADV 7YBO PRO A 444 UNP P22455 EXPRESSION TAG SEQADV 7YBO 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 CYS 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 IH7 A 801 42 HET SO4 A 802 5 HET SO4 A 803 5 HET SO4 A 804 5 HET SO4 A 805 5 HET SO4 A 806 5 HET SO4 A 807 5 HETNAM IH7 ~{N}-[4-[(1~{R})-1-[3,5-BIS(CHLORANYL)PYRIDIN-4- HETNAM 2 IH7 YL]ETHOXY]-5-CYANO-PYRIDIN-2-YL]-6-BROMANYL-5- HETNAM 3 IH7 (HYDROXYMETHYL)-1-(2-MORPHOLIN-4-YLETHYL)PYRROLO[3,2- HETNAM 4 IH7 B]PYRIDINE-3-CARBOXAMIDE HETNAM SO4 SULFATE ION FORMUL 2 IH7 C28 H24 BR CL2 N7 O4 FORMUL 3 SO4 6(O4 S 2-) FORMUL 9 HOH *61(H2 O) HELIX 1 AA1 PRO A 463 ASP A 465 5 3 HELIX 2 AA2 SER A 510 ILE A 527 1 18 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 THR A 684 1 18 HELIX 10 AB1 PRO A 694 GLU A 704 1 11 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 474 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 VAL A 548 N LYS A 503 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 CAJ IH7 A 801 1555 1555 1.66 CRYST1 40.075 60.440 59.899 90.00 94.93 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 0.024953 0.000000 0.002151 0.00000 SCALE2 0.000000 0.016545 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016757 0.00000