HEADER TRANSFERASE 11-JUL-23 8PQG TITLE C-KIT T670I MUTATED KINASE DOMAIN IN COMPLEX WITH AVAPRITINIB COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAST/STEM CELL GROWTH FACTOR RECEPTOR KIT; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: SCFR,PIEBALD TRAIT PROTEIN,PBT,PROTO-ONCOGENE C-KIT, COMPND 5 TYROSINE-PROTEIN KINASE KIT,P145 C-KIT,V-KIT HARDY-ZUCKERMAN 4 FELINE COMPND 6 SARCOMA VIRAL ONCOGENE HOMOLOG; COMPND 7 EC: 2.7.10.1; COMPND 8 ENGINEERED: YES; COMPND 9 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: KIT, SCFR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS C-KIT PROTEIN KINASE, AVAPRITINIB, INHIBITOR, TYROSINE KINASE, KEYWDS 2 TRANSMEMBRANE RECEPTOR, STEM CELL FACTOR, SCF, STEM CELL FACTOR KEYWDS 3 RECEPTOR, GIST, GASTROINTESTINAL STROMAL TUMORS, GATEKEEPER MUTANT, KEYWDS 4 GATEKEEPER MUTATION, P10721, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.TEUBER,M.P.MUELLER,D.RAUH REVDAT 4 07-AUG-24 8PQG 1 COMPND HETNAM HETSYN REVDAT 3 13-MAR-24 8PQG 1 REMARK REVDAT 2 17-JAN-24 8PQG 1 JRNL REVDAT 1 27-DEC-23 8PQG 0 JRNL AUTH A.TEUBER,T.SCHULZ,B.S.FLETCHER,R.GONTLA,T.MUHLENBERG, JRNL AUTH 2 M.L.ZISCHINSKY,J.NIGGENABER,J.WEISNER,S.B.KLEINBOLTING, JRNL AUTH 3 J.LATEGAHN,S.SIEVERS,M.P.MULLER,S.BAUER,D.RAUH JRNL TITL AVAPRITINIB-BASED SAR STUDIES UNVEIL A BINDING POCKET IN KIT JRNL TITL 2 AND PDGFRA. JRNL REF NAT COMMUN V. 15 63 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38167404 JRNL DOI 10.1038/S41467-023-44376-8 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 27015 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1351 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 48.1000 - 5.1700 1.00 2748 145 0.1756 0.1921 REMARK 3 2 5.1700 - 4.1000 1.00 2614 138 0.1603 0.1627 REMARK 3 3 4.1000 - 3.5800 1.00 2580 136 0.1794 0.2034 REMARK 3 4 3.5800 - 3.2600 1.00 2557 134 0.2153 0.2891 REMARK 3 5 3.2600 - 3.0200 1.00 2573 136 0.2608 0.2823 REMARK 3 6 3.0200 - 2.8500 1.00 2526 132 0.2713 0.3160 REMARK 3 7 2.8500 - 2.7000 1.00 2524 133 0.2721 0.2899 REMARK 3 8 2.7000 - 2.5900 1.00 2507 132 0.3148 0.3570 REMARK 3 9 2.5900 - 2.4900 0.99 2531 133 0.3205 0.3409 REMARK 3 10 2.4900 - 2.4000 0.99 2504 132 0.3354 0.3866 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.293 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.994 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 59.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.59 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 : 0.004 4821 REMARK 3 ANGLE : 0.587 6564 REMARK 3 CHIRALITY : 0.041 712 REMARK 3 PLANARITY : 0.005 899 REMARK 3 DIHEDRAL : 11.250 1779 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 566 THROUGH 765 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.6259 -21.8288 58.7572 REMARK 3 T TENSOR REMARK 3 T11: 0.4862 T22: 0.3775 REMARK 3 T33: 0.4921 T12: 0.0436 REMARK 3 T13: 0.0293 T23: -0.0423 REMARK 3 L TENSOR REMARK 3 L11: 2.1902 L22: 2.2695 REMARK 3 L33: 2.3488 L12: -0.1565 REMARK 3 L13: 0.4401 L23: 0.2324 REMARK 3 S TENSOR REMARK 3 S11: -0.1050 S12: -0.1641 S13: -0.1798 REMARK 3 S21: 0.1051 S22: -0.0726 S23: 0.1954 REMARK 3 S31: -0.0121 S32: -0.2545 S33: 0.1679 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 766 THROUGH 931 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.7420 -26.6001 37.5369 REMARK 3 T TENSOR REMARK 3 T11: 0.5197 T22: 0.4461 REMARK 3 T33: 0.4586 T12: 0.0352 REMARK 3 T13: -0.0359 T23: -0.0278 REMARK 3 L TENSOR REMARK 3 L11: 2.0264 L22: 4.7683 REMARK 3 L33: 3.7096 L12: -1.2589 REMARK 3 L13: -0.7023 L23: 1.5641 REMARK 3 S TENSOR REMARK 3 S11: 0.0633 S12: 0.0505 S13: 0.1448 REMARK 3 S21: -0.3653 S22: -0.2353 S23: 0.3186 REMARK 3 S31: -0.5742 S32: -0.1721 S33: 0.1400 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 565 THROUGH 600 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.1804 -5.9541 -13.6360 REMARK 3 T TENSOR REMARK 3 T11: 0.4703 T22: 0.5284 REMARK 3 T33: 0.3836 T12: 0.0066 REMARK 3 T13: 0.0000 T23: -0.0291 REMARK 3 L TENSOR REMARK 3 L11: 1.7063 L22: 2.9537 REMARK 3 L33: 3.2797 L12: 1.1272 REMARK 3 L13: -0.2232 L23: -0.4460 REMARK 3 S TENSOR REMARK 3 S11: -0.0952 S12: 0.2133 S13: -0.1809 REMARK 3 S21: -0.5584 S22: 0.0237 S23: -0.1570 REMARK 3 S31: 0.1909 S32: -0.1829 S33: -0.0151 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 601 THROUGH 630 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.5828 5.9100 -16.0096 REMARK 3 T TENSOR REMARK 3 T11: 0.6816 T22: 0.5951 REMARK 3 T33: 0.5255 T12: -0.0395 REMARK 3 T13: 0.0432 T23: 0.0598 REMARK 3 L TENSOR REMARK 3 L11: 2.2061 L22: 3.5102 REMARK 3 L33: 5.3400 L12: 1.0153 REMARK 3 L13: -0.2305 L23: 0.4704 REMARK 3 S TENSOR REMARK 3 S11: -0.1363 S12: 0.2307 S13: 0.1852 REMARK 3 S21: -0.3895 S22: -0.0434 S23: -0.1745 REMARK 3 S31: -0.4261 S32: -0.2329 S33: -0.0665 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 631 THROUGH 677 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.0597 -1.2304 -9.7339 REMARK 3 T TENSOR REMARK 3 T11: 0.5339 T22: 0.5301 REMARK 3 T33: 0.5209 T12: -0.0014 REMARK 3 T13: -0.0369 T23: 0.0397 REMARK 3 L TENSOR REMARK 3 L11: 2.6232 L22: 3.6961 REMARK 3 L33: 4.8510 L12: 0.7068 REMARK 3 L13: 0.3477 L23: 0.4024 REMARK 3 S TENSOR REMARK 3 S11: 0.0810 S12: 0.0079 S13: -0.1184 REMARK 3 S21: -0.2500 S22: -0.0202 S23: 0.0980 REMARK 3 S31: 0.0063 S32: -0.2577 S33: -0.0196 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 678 THROUGH 808 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.3958 8.1072 7.5159 REMARK 3 T TENSOR REMARK 3 T11: 0.5006 T22: 0.4880 REMARK 3 T33: 0.4663 T12: 0.0629 REMARK 3 T13: 0.0386 T23: 0.0222 REMARK 3 L TENSOR REMARK 3 L11: 2.3729 L22: 3.4236 REMARK 3 L33: 4.2730 L12: 0.5083 REMARK 3 L13: -0.2308 L23: 0.5044 REMARK 3 S TENSOR REMARK 3 S11: 0.1267 S12: -0.0716 S13: 0.3458 REMARK 3 S21: -0.0773 S22: -0.1028 S23: 0.2245 REMARK 3 S31: -0.5582 S32: -0.2287 S33: -0.0149 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 809 THROUGH 828 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.9060 -12.8662 0.3377 REMARK 3 T TENSOR REMARK 3 T11: 0.8692 T22: 0.7960 REMARK 3 T33: 0.7132 T12: 0.1038 REMARK 3 T13: 0.0655 T23: 0.0103 REMARK 3 L TENSOR REMARK 3 L11: 1.5542 L22: 2.7431 REMARK 3 L33: 0.7864 L12: 1.7349 REMARK 3 L13: 0.9889 L23: 1.4069 REMARK 3 S TENSOR REMARK 3 S11: 0.2415 S12: 0.2132 S13: -0.5912 REMARK 3 S21: -0.4486 S22: -0.4862 S23: 0.0305 REMARK 3 S31: 0.9999 S32: 0.5303 S33: -0.1017 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 829 THROUGH 916 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.3371 -3.1725 15.3150 REMARK 3 T TENSOR REMARK 3 T11: 0.4371 T22: 0.3622 REMARK 3 T33: 0.3649 T12: 0.0179 REMARK 3 T13: 0.0013 T23: -0.0285 REMARK 3 L TENSOR REMARK 3 L11: 3.7219 L22: 3.2900 REMARK 3 L33: 2.8607 L12: -1.2630 REMARK 3 L13: 0.1973 L23: -0.1367 REMARK 3 S TENSOR REMARK 3 S11: -0.0718 S12: -0.0831 S13: 0.2019 REMARK 3 S21: 0.2435 S22: 0.0549 S23: -0.2503 REMARK 3 S31: 0.0469 S32: -0.0650 S33: 0.0074 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 917 THROUGH 932 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.3027 3.4967 18.6275 REMARK 3 T TENSOR REMARK 3 T11: 0.5996 T22: 0.8925 REMARK 3 T33: 0.7552 T12: -0.0123 REMARK 3 T13: -0.0337 T23: -0.0300 REMARK 3 L TENSOR REMARK 3 L11: 4.9517 L22: 5.1787 REMARK 3 L33: 3.8181 L12: -1.7086 REMARK 3 L13: 0.7065 L23: 0.0452 REMARK 3 S TENSOR REMARK 3 S11: -0.2190 S12: -0.5264 S13: 0.4789 REMARK 3 S21: 0.6657 S22: -0.2098 S23: 0.5661 REMARK 3 S31: -0.4341 S32: -0.7965 S33: 0.1457 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 8PQG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292130379. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-AUG-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27017 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 48.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.92 REMARK 200 R MERGE (I) : NULL 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) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 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 : 1.210 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6 MG/ML, 25% PEG3350, 200 MM NA REMARK 280 -CITRATE, 100 MM BIS-TRIS-PROPANE, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 29.37500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 96.21000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.54500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 96.21000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.37500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.54500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 548 REMARK 465 SER A 549 REMARK 465 MET A 550 REMARK 465 PRO A 551 REMARK 465 MET A 552 REMARK 465 TYR A 553 REMARK 465 GLU A 554 REMARK 465 VAL A 555 REMARK 465 GLN A 556 REMARK 465 TRP A 557 REMARK 465 LYS A 558 REMARK 465 VAL A 559 REMARK 465 VAL A 560 REMARK 465 GLU A 561 REMARK 465 GLU A 562 REMARK 465 SER A 563 REMARK 465 ASN A 564 REMARK 465 GLY A 565 REMARK 465 VAL A 754 REMARK 465 ALA A 755 REMARK 465 PRO A 756 REMARK 465 GLU A 757 REMARK 465 ASP A 758 REMARK 465 LEU A 759 REMARK 465 TYR A 760 REMARK 465 LYS A 761 REMARK 465 ASP A 762 REMARK 465 ASN A 819 REMARK 465 ASP A 820 REMARK 465 LYS A 826 REMARK 465 GLY A 827 REMARK 465 ASN A 828 REMARK 465 THR A 932 REMARK 465 ASN A 933 REMARK 465 HIS A 934 REMARK 465 GLY C 548 REMARK 465 SER C 549 REMARK 465 MET C 550 REMARK 465 PRO C 551 REMARK 465 MET C 552 REMARK 465 TYR C 553 REMARK 465 GLU C 554 REMARK 465 VAL C 555 REMARK 465 GLN C 556 REMARK 465 TRP C 557 REMARK 465 LYS C 558 REMARK 465 VAL C 559 REMARK 465 VAL C 560 REMARK 465 GLU C 561 REMARK 465 GLU C 562 REMARK 465 SER C 563 REMARK 465 ASN C 564 REMARK 465 VAL C 754 REMARK 465 ALA C 755 REMARK 465 PRO C 756 REMARK 465 GLU C 757 REMARK 465 ASP C 758 REMARK 465 LEU C 759 REMARK 465 TYR C 760 REMARK 465 LYS C 761 REMARK 465 ASN C 933 REMARK 465 HIS C 934 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 ASN A 566 CG OD1 ND2 REMARK 470 LYS A 593 CG CD CE NZ REMARK 470 PHE A 600 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 613 CG CD CE NZ REMARK 470 HIS A 630 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 633 CG CD OE1 OE2 REMARK 470 ARG A 634 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 687 CG OD1 OD2 REMARK 470 GLU A 688 CG CD OE1 OE2 REMARK 470 TYR A 692 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 693 CG CD CE NZ REMARK 470 PHE A 763 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 818 CG CD CE NZ REMARK 470 SER A 821 OG REMARK 470 LYS A 918 CG CD CE NZ REMARK 470 LYS A 926 CG CD CE NZ REMARK 470 GLU A 930 CG CD OE1 OE2 REMARK 470 SER A 931 OG REMARK 470 ASN C 566 CG OD1 ND2 REMARK 470 LYS C 593 CG CD CE NZ REMARK 470 PHE C 600 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ILE C 612 CG1 CG2 CD1 REMARK 470 LYS C 613 CG CD CE NZ REMARK 470 SER C 614 OG REMARK 470 ASP C 615 CG OD1 OD2 REMARK 470 ASP C 687 CG OD1 OD2 REMARK 470 GLU C 688 CG CD OE1 OE2 REMARK 470 LYS C 693 CG CD CE NZ REMARK 470 ASP C 762 CG OD1 OD2 REMARK 470 LYS C 818 CG CD CE NZ REMARK 470 ASP C 820 CG OD1 OD2 REMARK 470 LYS C 826 CG CD CE NZ REMARK 470 ASN C 828 CG OD1 ND2 REMARK 470 LYS C 878 CG CD CE NZ REMARK 470 GLN C 922 CG CD OE1 NE2 REMARK 470 LYS C 926 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 GLU A 688 75.18 -116.43 REMARK 500 ARG A 791 -5.78 71.94 REMARK 500 ASP A 792 45.94 -143.23 REMARK 500 THR A 801 -166.27 -129.27 REMARK 500 ASP A 810 78.46 54.99 REMARK 500 VAL A 875 98.14 -69.65 REMARK 500 ASP C 792 41.83 -145.84 REMARK 500 THR C 801 -162.83 -119.82 REMARK 500 ASP C 810 81.81 59.69 REMARK 500 REMARK 500 REMARK: NULL DBREF 8PQG A 551 687 UNP P10721 KIT_HUMAN 551 687 DBREF 8PQG A 766 934 UNP P10721 KIT_HUMAN 766 934 DBREF 8PQG C 551 687 UNP P10721 KIT_HUMAN 551 687 DBREF 8PQG C 766 934 UNP P10721 KIT_HUMAN 766 934 SEQADV 8PQG GLY A 548 UNP P10721 EXPRESSION TAG SEQADV 8PQG SER A 549 UNP P10721 EXPRESSION TAG SEQADV 8PQG MET A 550 UNP P10721 EXPRESSION TAG SEQADV 8PQG SER A 563 UNP P10721 ILE 563 ENGINEERED MUTATION SEQADV 8PQG SER A 569 UNP P10721 VAL 569 ENGINEERED MUTATION SEQADV 8PQG GLN A 609 UNP P10721 TYR 609 ENGINEERED MUTATION SEQADV 8PQG SER A 631 UNP P10721 LEU 631 ENGINEERED MUTATION SEQADV 8PQG GLU A 651 UNP P10721 MET 651 ENGINEERED MUTATION SEQADV 8PQG HIS A 662 UNP P10721 ILE 662 ENGINEERED MUTATION SEQADV 8PQG ILE A 670 UNP P10721 THR 670 ENGINEERED MUTATION SEQADV 8PQG GLU A 688 UNP P10721 LINKER SEQADV 8PQG PHE A 689 UNP P10721 LINKER SEQADV 8PQG VAL A 690 UNP P10721 LINKER SEQADV 8PQG PRO A 691 UNP P10721 LINKER SEQADV 8PQG TYR A 692 UNP P10721 LINKER SEQADV 8PQG LYS A 693 UNP P10721 LINKER SEQADV 8PQG VAL A 754 UNP P10721 LINKER SEQADV 8PQG ALA A 755 UNP P10721 LINKER SEQADV 8PQG PRO A 756 UNP P10721 LINKER SEQADV 8PQG GLU A 757 UNP P10721 LINKER SEQADV 8PQG ASP A 758 UNP P10721 LINKER SEQADV 8PQG LEU A 759 UNP P10721 LINKER SEQADV 8PQG TYR A 760 UNP P10721 LINKER SEQADV 8PQG LYS A 761 UNP P10721 LINKER SEQADV 8PQG ASP A 762 UNP P10721 LINKER SEQADV 8PQG PHE A 763 UNP P10721 LINKER SEQADV 8PQG LEU A 764 UNP P10721 LINKER SEQADV 8PQG THR A 765 UNP P10721 LINKER SEQADV 8PQG HIS A 768 UNP P10721 ASP 768 ENGINEERED MUTATION SEQADV 8PQG ASN A 804 UNP P10721 ARG 804 ENGINEERED MUTATION SEQADV 8PQG ASP A 825 UNP P10721 VAL 825 ENGINEERED MUTATION SEQADV 8PQG SER A 844 UNP P10721 CYS 844 ENGINEERED MUTATION SEQADV 8PQG SER A 890 UNP P10721 LEU 890 ENGINEERED MUTATION SEQADV 8PQG TYR A 894 UNP P10721 HIS 894 ENGINEERED MUTATION SEQADV 8PQG ASP A 912 UNP P10721 LEU 912 ENGINEERED MUTATION SEQADV 8PQG ASP A 923 UNP P10721 LEU 923 ENGINEERED MUTATION SEQADV 8PQG GLY C 548 UNP P10721 EXPRESSION TAG SEQADV 8PQG SER C 549 UNP P10721 EXPRESSION TAG SEQADV 8PQG MET C 550 UNP P10721 EXPRESSION TAG SEQADV 8PQG SER C 563 UNP P10721 ILE 563 ENGINEERED MUTATION SEQADV 8PQG SER C 569 UNP P10721 VAL 569 ENGINEERED MUTATION SEQADV 8PQG GLN C 609 UNP P10721 TYR 609 ENGINEERED MUTATION SEQADV 8PQG SER C 631 UNP P10721 LEU 631 ENGINEERED MUTATION SEQADV 8PQG GLU C 651 UNP P10721 MET 651 ENGINEERED MUTATION SEQADV 8PQG HIS C 662 UNP P10721 ILE 662 ENGINEERED MUTATION SEQADV 8PQG ILE C 670 UNP P10721 THR 670 ENGINEERED MUTATION SEQADV 8PQG GLU C 688 UNP P10721 LINKER SEQADV 8PQG PHE C 689 UNP P10721 LINKER SEQADV 8PQG VAL C 690 UNP P10721 LINKER SEQADV 8PQG PRO C 691 UNP P10721 LINKER SEQADV 8PQG TYR C 692 UNP P10721 LINKER SEQADV 8PQG LYS C 693 UNP P10721 LINKER SEQADV 8PQG VAL C 754 UNP P10721 LINKER SEQADV 8PQG ALA C 755 UNP P10721 LINKER SEQADV 8PQG PRO C 756 UNP P10721 LINKER SEQADV 8PQG GLU C 757 UNP P10721 LINKER SEQADV 8PQG ASP C 758 UNP P10721 LINKER SEQADV 8PQG LEU C 759 UNP P10721 LINKER SEQADV 8PQG TYR C 760 UNP P10721 LINKER SEQADV 8PQG LYS C 761 UNP P10721 LINKER SEQADV 8PQG ASP C 762 UNP P10721 LINKER SEQADV 8PQG PHE C 763 UNP P10721 LINKER SEQADV 8PQG LEU C 764 UNP P10721 LINKER SEQADV 8PQG THR C 765 UNP P10721 LINKER SEQADV 8PQG HIS C 768 UNP P10721 ASP 768 ENGINEERED MUTATION SEQADV 8PQG ASN C 804 UNP P10721 ARG 804 ENGINEERED MUTATION SEQADV 8PQG ASP C 825 UNP P10721 VAL 825 ENGINEERED MUTATION SEQADV 8PQG SER C 844 UNP P10721 CYS 844 ENGINEERED MUTATION SEQADV 8PQG SER C 890 UNP P10721 LEU 890 ENGINEERED MUTATION SEQADV 8PQG TYR C 894 UNP P10721 HIS 894 ENGINEERED MUTATION SEQADV 8PQG ASP C 912 UNP P10721 LEU 912 ENGINEERED MUTATION SEQADV 8PQG ASP C 923 UNP P10721 LEU 923 ENGINEERED MUTATION SEQRES 1 A 327 GLY SER MET PRO MET TYR GLU VAL GLN TRP LYS VAL VAL SEQRES 2 A 327 GLU GLU SER ASN GLY ASN ASN TYR SER TYR ILE ASP PRO SEQRES 3 A 327 THR GLN LEU PRO TYR ASP HIS LYS TRP GLU PHE PRO ARG SEQRES 4 A 327 ASN ARG LEU SER PHE GLY LYS THR LEU GLY ALA GLY ALA SEQRES 5 A 327 PHE GLY LYS VAL VAL GLU ALA THR ALA GLN GLY LEU ILE SEQRES 6 A 327 LYS SER ASP ALA ALA MET THR VAL ALA VAL LYS MET LEU SEQRES 7 A 327 LYS PRO SER ALA HIS SER THR GLU ARG GLU ALA LEU MET SEQRES 8 A 327 SER GLU LEU LYS VAL LEU SER TYR LEU GLY ASN HIS GLU SEQRES 9 A 327 ASN ILE VAL ASN LEU LEU GLY ALA CYS THR HIS GLY GLY SEQRES 10 A 327 PRO THR LEU VAL ILE ILE GLU TYR CYS CYS TYR GLY ASP SEQRES 11 A 327 LEU LEU ASN PHE LEU ARG ARG LYS ARG ASP GLU PHE VAL SEQRES 12 A 327 PRO TYR LYS VAL ALA PRO GLU ASP LEU TYR LYS ASP PHE SEQRES 13 A 327 LEU THR LEU GLU HIS LEU LEU SER PHE SER TYR GLN VAL SEQRES 14 A 327 ALA LYS GLY MET ALA PHE LEU ALA SER LYS ASN CYS ILE SEQRES 15 A 327 HIS ARG ASP LEU ALA ALA ARG ASN ILE LEU LEU THR HIS SEQRES 16 A 327 GLY ASN ILE THR LYS ILE CYS ASP PHE GLY LEU ALA ARG SEQRES 17 A 327 ASP ILE LYS ASN ASP SER ASN TYR VAL ASP LYS GLY ASN SEQRES 18 A 327 ALA ARG LEU PRO VAL LYS TRP MET ALA PRO GLU SER ILE SEQRES 19 A 327 PHE ASN SER VAL TYR THR PHE GLU SER ASP VAL TRP SER SEQRES 20 A 327 TYR GLY ILE PHE LEU TRP GLU LEU PHE SER LEU GLY SER SEQRES 21 A 327 SER PRO TYR PRO GLY MET PRO VAL ASP SER LYS PHE TYR SEQRES 22 A 327 LYS MET ILE LYS GLU GLY PHE ARG MET SER SER PRO GLU SEQRES 23 A 327 TYR ALA PRO ALA GLU MET TYR ASP ILE MET LYS THR CYS SEQRES 24 A 327 TRP ASP ALA ASP PRO ASP LYS ARG PRO THR PHE LYS GLN SEQRES 25 A 327 ILE VAL GLN ASP ILE GLU LYS GLN ILE SER GLU SER THR SEQRES 26 A 327 ASN HIS SEQRES 1 C 327 GLY SER MET PRO MET TYR GLU VAL GLN TRP LYS VAL VAL SEQRES 2 C 327 GLU GLU SER ASN GLY ASN ASN TYR SER TYR ILE ASP PRO SEQRES 3 C 327 THR GLN LEU PRO TYR ASP HIS LYS TRP GLU PHE PRO ARG SEQRES 4 C 327 ASN ARG LEU SER PHE GLY LYS THR LEU GLY ALA GLY ALA SEQRES 5 C 327 PHE GLY LYS VAL VAL GLU ALA THR ALA GLN GLY LEU ILE SEQRES 6 C 327 LYS SER ASP ALA ALA MET THR VAL ALA VAL LYS MET LEU SEQRES 7 C 327 LYS PRO SER ALA HIS SER THR GLU ARG GLU ALA LEU MET SEQRES 8 C 327 SER GLU LEU LYS VAL LEU SER TYR LEU GLY ASN HIS GLU SEQRES 9 C 327 ASN ILE VAL ASN LEU LEU GLY ALA CYS THR HIS GLY GLY SEQRES 10 C 327 PRO THR LEU VAL ILE ILE GLU TYR CYS CYS TYR GLY ASP SEQRES 11 C 327 LEU LEU ASN PHE LEU ARG ARG LYS ARG ASP GLU PHE VAL SEQRES 12 C 327 PRO TYR LYS VAL ALA PRO GLU ASP LEU TYR LYS ASP PHE SEQRES 13 C 327 LEU THR LEU GLU HIS LEU LEU SER PHE SER TYR GLN VAL SEQRES 14 C 327 ALA LYS GLY MET ALA PHE LEU ALA SER LYS ASN CYS ILE SEQRES 15 C 327 HIS ARG ASP LEU ALA ALA ARG ASN ILE LEU LEU THR HIS SEQRES 16 C 327 GLY ASN ILE THR LYS ILE CYS ASP PHE GLY LEU ALA ARG SEQRES 17 C 327 ASP ILE LYS ASN ASP SER ASN TYR VAL ASP LYS GLY ASN SEQRES 18 C 327 ALA ARG LEU PRO VAL LYS TRP MET ALA PRO GLU SER ILE SEQRES 19 C 327 PHE ASN SER VAL TYR THR PHE GLU SER ASP VAL TRP SER SEQRES 20 C 327 TYR GLY ILE PHE LEU TRP GLU LEU PHE SER LEU GLY SER SEQRES 21 C 327 SER PRO TYR PRO GLY MET PRO VAL ASP SER LYS PHE TYR SEQRES 22 C 327 LYS MET ILE LYS GLU GLY PHE ARG MET SER SER PRO GLU SEQRES 23 C 327 TYR ALA PRO ALA GLU MET TYR ASP ILE MET LYS THR CYS SEQRES 24 C 327 TRP ASP ALA ASP PRO ASP LYS ARG PRO THR PHE LYS GLN SEQRES 25 C 327 ILE VAL GLN ASP ILE GLU LYS GLN ILE SER GLU SER THR SEQRES 26 C 327 ASN HIS HET 9JI A1001 37 HET 9JI C1001 37 HETNAM 9JI AVAPRITINIB HETSYN 9JI (1~{S})-1-(4-FLUOROPHENYL)-1-[2-[4-[6-(1-METHYLPYRAZOL- HETSYN 2 9JI 4-YL)PYRROLO[2,1-F][1,2,4]TRIAZIN-4-YL]PIPERAZIN-1- HETSYN 3 9JI YL]PYRIMIDIN-5-YL]ETHANAMINE FORMUL 3 9JI 2(C26 H27 F N10) FORMUL 5 HOH *42(H2 O) HELIX 1 AA1 ASP A 572 LEU A 576 5 5 HELIX 2 AA2 ASP A 579 GLU A 583 5 5 HELIX 3 AA3 PRO A 585 ASN A 587 5 3 HELIX 4 AA4 HIS A 630 GLY A 648 1 19 HELIX 5 AA5 LEU A 678 ARG A 686 1 9 HELIX 6 AA6 LEU A 766 LYS A 786 1 21 HELIX 7 AA7 ALA A 794 ARG A 796 5 3 HELIX 8 AA8 HIS A 802 ASN A 804 5 3 HELIX 9 AA9 PRO A 832 MET A 836 5 5 HELIX 10 AB1 ALA A 837 SER A 844 1 8 HELIX 11 AB2 THR A 847 SER A 864 1 18 HELIX 12 AB3 ASP A 876 GLY A 886 1 11 HELIX 13 AB4 PRO A 896 TRP A 907 1 12 HELIX 14 AB5 ASP A 910 ARG A 914 5 5 HELIX 15 AB6 THR A 916 SER A 931 1 16 HELIX 16 AB7 ASP C 572 LEU C 576 5 5 HELIX 17 AB8 ASP C 579 GLU C 583 5 5 HELIX 18 AB9 PRO C 585 ASN C 587 5 3 HELIX 19 AC1 HIS C 630 GLY C 648 1 19 HELIX 20 AC2 LEU C 678 ARG C 686 1 9 HELIX 21 AC3 ASP C 687 PHE C 689 5 3 HELIX 22 AC4 THR C 765 LYS C 786 1 22 HELIX 23 AC5 ALA C 794 ARG C 796 5 3 HELIX 24 AC6 HIS C 802 ASN C 804 5 3 HELIX 25 AC7 PRO C 832 MET C 836 5 5 HELIX 26 AC8 ALA C 837 SER C 844 1 8 HELIX 27 AC9 THR C 847 SER C 864 1 18 HELIX 28 AD1 ASP C 876 GLY C 886 1 11 HELIX 29 AD2 PRO C 896 TRP C 907 1 12 HELIX 30 AD3 ASP C 910 ARG C 914 5 5 HELIX 31 AD4 THR C 916 THR C 932 1 17 SHEET 1 AA1 5 LEU A 589 ALA A 597 0 SHEET 2 AA1 5 GLY A 601 GLN A 609 -1 O GLU A 605 N LYS A 593 SHEET 3 AA1 5 ALA A 617 LEU A 625 -1 O MET A 618 N ALA A 608 SHEET 4 AA1 5 LEU A 667 GLU A 671 -1 O ILE A 670 N ALA A 621 SHEET 5 AA1 5 LEU A 656 CYS A 660 -1 N LEU A 657 O ILE A 669 SHEET 1 AA2 3 GLY A 676 ASP A 677 0 SHEET 2 AA2 3 ILE A 798 THR A 801 -1 O LEU A 800 N GLY A 676 SHEET 3 AA2 3 ILE A 805 ILE A 808 -1 O LYS A 807 N LEU A 799 SHEET 1 AA3 2 PHE A 689 VAL A 690 0 SHEET 2 AA3 2 LEU A 764 THR A 765 1 O LEU A 764 N VAL A 690 SHEET 1 AA4 2 CYS A 788 ILE A 789 0 SHEET 2 AA4 2 ARG A 815 ASP A 816 -1 O ARG A 815 N ILE A 789 SHEET 1 AA5 2 TYR A 823 VAL A 824 0 SHEET 2 AA5 2 VAL A 845 TYR A 846 -1 O TYR A 846 N TYR A 823 SHEET 1 AA6 5 LEU C 589 ALA C 597 0 SHEET 2 AA6 5 GLY C 601 GLN C 609 -1 O GLU C 605 N GLY C 592 SHEET 3 AA6 5 ALA C 617 LEU C 625 -1 O VAL C 620 N ALA C 606 SHEET 4 AA6 5 LEU C 667 GLU C 671 -1 O ILE C 670 N ALA C 621 SHEET 5 AA6 5 LEU C 656 CYS C 660 -1 N LEU C 657 O ILE C 669 SHEET 1 AA7 3 GLY C 676 ASP C 677 0 SHEET 2 AA7 3 ILE C 798 LEU C 800 -1 O LEU C 800 N GLY C 676 SHEET 3 AA7 3 THR C 806 ILE C 808 -1 O LYS C 807 N LEU C 799 SHEET 1 AA8 2 CYS C 788 ILE C 789 0 SHEET 2 AA8 2 ARG C 815 ASP C 816 -1 O ARG C 815 N ILE C 789 SHEET 1 AA9 2 TYR C 823 VAL C 824 0 SHEET 2 AA9 2 VAL C 845 TYR C 846 -1 O TYR C 846 N TYR C 823 CRYST1 58.750 59.090 192.420 90.00 90.00 90.00 P 21 21 21 8 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 0.017021 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016923 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005197 0.00000