HEADER TRANSFERASE-TRANSFERASE INHIBITOR 16-JUN-21 7F3M TITLE CRYSTAL STRUCTURE OF FGFR4 KINASE DOMAIN WITH PRN1371 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 K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS KINASE, INHIBITOR, COMPLEX, STRUCTURAL PROTEIN, TRANSFERASE- KEYWDS 2 TRANSFERASE INHIBITOR COMPLEX, TRANSFERASE-TRANSFERASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR X.J.CHEN,L.Z.QU,S.Y.DAI,H.D.WEI,Y.H.CHEN REVDAT 4 29-NOV-23 7F3M 1 REMARK REVDAT 3 09-MAR-22 7F3M 1 JRNL REVDAT 2 26-JAN-22 7F3M 1 JRNL REVDAT 1 12-JAN-22 7F3M 0 JRNL AUTH L.QU,X.CHEN,H.WEI,M.GUO,S.DAI,L.JIANG,J.LI,S.YUE,Z.CHEN, JRNL AUTH 2 Y.CHEN JRNL TITL STRUCTURAL INSIGHTS INTO THE POTENCY AND SELECTIVITY OF JRNL TITL 2 COVALENT PAN-FGFR INHIBITORS JRNL REF COMMUN CHEM V. 5 5 2022 JRNL REFN ESSN 2399-3669 JRNL DOI 10.1038/S42004-021-00623-X REMARK 2 REMARK 2 RESOLUTION. 2.29 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) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 13012 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 642 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 42.9900 - 3.9129 0.98 2640 157 0.1618 0.1978 REMARK 3 2 3.9129 - 3.1061 0.98 2644 128 0.1702 0.2274 REMARK 3 3 3.1061 - 2.7135 0.98 2600 139 0.2126 0.2751 REMARK 3 4 2.7135 - 2.4654 0.93 2471 124 0.2314 0.2933 REMARK 3 5 2.4654 - 2.2890 0.74 2008 94 0.2427 0.3287 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.73 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 2458 REMARK 3 ANGLE : 0.694 3337 REMARK 3 CHIRALITY : 0.026 354 REMARK 3 PLANARITY : 0.003 430 REMARK 3 DIHEDRAL : 13.958 945 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 7F3M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022780. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 85 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-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13012 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.289 REMARK 200 RESOLUTION RANGE LOW (A) : 42.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.09191 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.24410 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.870 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: 4QRC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS (PH 4.5), 0.2 M LI2SO4, REMARK 280 18 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.15K 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 30.55000 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: 220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 PHE A 478 REMARK 465 GLY A 569 REMARK 465 PRO A 570 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 1217 O HOH A 1238 2.16 REMARK 500 O HOH A 1208 O HOH A 1224 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 475 -68.61 -94.49 REMARK 500 ASN A 508 65.17 67.49 REMARK 500 SER A 580 31.64 -95.79 REMARK 500 ARG A 611 -0.81 71.34 REMARK 500 ASP A 612 51.25 -155.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 616 0.28 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 7F3M A 445 753 UNP P22455 FGFR4_HUMAN 445 753 SEQADV 7F3M GLY A 443 UNP P22455 EXPRESSION TAG SEQADV 7F3M PRO A 444 UNP P22455 EXPRESSION TAG SEQADV 7F3M 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 GX3 A 801 38 HET SO4 A 802 5 HET SO4 A 803 5 HET SO4 A 804 5 HETNAM GX3 6-[2,6-BIS(CHLORANYL)-3,5-DIMETHOXY-PHENYL]-2- HETNAM 2 GX3 (METHYLAMINO)-8-[3-(4-PROP-2-ENOYLPIPERAZIN-1-YL) HETNAM 3 GX3 PROPYL]PYRIDO[2,3-D]PYRIMIDIN-7-ONE HETNAM SO4 SULFATE ION HETSYN GX3 PRN1371 FORMUL 2 GX3 C26 H30 CL2 N6 O4 FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *144(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 PHE A 662 1 6 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 ALA A 749 1 15 SHEET 1 AA1 5 LEU A 467 PRO A 472 0 SHEET 2 AA1 5 GLN A 480 PHE A 487 -1 O ARG A 483 N LYS A 471 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 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 CRYST1 42.449 61.100 61.041 90.00 97.65 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 0.023558 0.000000 0.003165 0.00000 SCALE2 0.000000 0.016367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016530 0.00000