PDB Short entry for 3CPC HEADER TRANSFERASE 31-MAR-08 3CPC TITLE CRYSTAL STRUCTURE OF THE VEGFR2 KINASE DOMAIN IN COMPLEX WITH A TITLE 2 PYRIDONE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PROTEIN KINASE DOMAIN, RESIDUES 940-989 DELETED; COMPND 5 SYNONYM: VEGFR-2, KINASE INSERT DOMAIN RECEPTOR, PROTEIN-TYROSINE COMPND 6 KINASE RECEPTOR FLK-1, CD309 ANTIGEN; 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: KDR, FLK1; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS RECEPTOR TYROSINE KINASE, ANGIOGENESIS, ATP-BINDING, DEVELOPMENTAL KEYWDS 2 PROTEIN, DIFFERENTIATION, GLYCOPROTEIN, HOST-VIRUS INTERACTION, KEYWDS 3 IMMUNOGLOBULIN DOMAIN, MEMBRANE, NUCLEOTIDE-BINDING, PHOSPHOPROTEIN, KEYWDS 4 TRANSFERASE, TRANSMEMBRANE, TYROSINE-PROTEIN KINASE EXPDTA X-RAY DIFFRACTION AUTHOR D.A.WHITTINGTON,A.M.LONG,P.ROSE,Y.GU,H.ZHAO REVDAT 6 20-OCT-21 3CPC 1 REMARK SEQADV REVDAT 5 13-JUN-18 3CPC 1 DBREF SEQADV REVDAT 4 26-JUL-17 3CPC 1 SOURCE REMARK REVDAT 3 13-JUL-11 3CPC 1 VERSN REVDAT 2 24-FEB-09 3CPC 1 VERSN REVDAT 1 17-JUN-08 3CPC 0 JRNL AUTH E.HU,A.TASKER,R.D.WHITE,R.K.KUNZ,J.HUMAN,N.CHEN,R.BURLI, JRNL AUTH 2 R.HUNGATE,P.NOVAK,A.ITANO,X.ZHANG,V.YU,Y.NGUYEN,Y.TUDOR, JRNL AUTH 3 M.PLANT,S.FLYNN,Y.XU,K.L.MEAGHER,D.A.WHITTINGTON,G.Y.NG JRNL TITL DISCOVERY OF ARYL AMINOQUINAZOLINE PYRIDONES AS POTENT, JRNL TITL 2 SELECTIVE, AND ORALLY EFFICACIOUS INHIBITORS OF RECEPTOR JRNL TITL 3 TYROSINE KINASE C-KIT. JRNL REF J.MED.CHEM. V. 51 3065 2008 JRNL REFN ISSN 0022-2623 JRNL PMID 18447379 JRNL DOI 10.1021/JM800188G REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 22627 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1422 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.47 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1631 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4409 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 113 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.24000 REMARK 3 B22 (A**2) : -0.89000 REMARK 3 B33 (A**2) : 2.17000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.33000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.307 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.205 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.089 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4584 ; 0.007 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6204 ; 0.933 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 538 ; 4.985 ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 203 ;32.395 ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 800 ;12.869 ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;14.484 ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 671 ; 0.061 ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3439 ; 0.002 ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1992 ; 0.162 ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3092 ; 0.295 ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 184 ; 0.112 ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 46 ; 0.133 ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.166 ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2827 ; 0.574 ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4398 ; 1.000 ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2071 ; 0.677 ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1806 ; 1.077 ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 820 A 1178 REMARK 3 ORIGIN FOR THE GROUP (A): 4.7018 36.3372 32.7060 REMARK 3 T TENSOR REMARK 3 T11: -0.0277 T22: -0.0257 REMARK 3 T33: -0.0163 T12: 0.0010 REMARK 3 T13: -0.0147 T23: -0.0216 REMARK 3 L TENSOR REMARK 3 L11: 1.2190 L22: 0.1251 REMARK 3 L33: 0.0065 L12: 0.0185 REMARK 3 L13: 0.0655 L23: -0.0031 REMARK 3 S TENSOR REMARK 3 S11: -0.0249 S12: -0.0570 S13: -0.0345 REMARK 3 S21: -0.0391 S22: 0.0143 S23: -0.0198 REMARK 3 S31: -0.0029 S32: 0.0073 S33: 0.0106 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 820 B 1165 REMARK 3 ORIGIN FOR THE GROUP (A): 20.2856 2.2431 12.4638 REMARK 3 T TENSOR REMARK 3 T11: 0.0130 T22: -0.0932 REMARK 3 T33: -0.0855 T12: 0.0169 REMARK 3 T13: 0.0538 T23: 0.0082 REMARK 3 L TENSOR REMARK 3 L11: 2.0156 L22: 1.2324 REMARK 3 L33: 0.9448 L12: 0.9683 REMARK 3 L13: 0.4120 L23: 0.2609 REMARK 3 S TENSOR REMARK 3 S11: -0.1334 S12: 0.0944 S13: 0.0928 REMARK 3 S21: -0.1790 S22: 0.0016 S23: -0.0620 REMARK 3 S31: 0.1252 S32: -0.0148 S33: 0.1319 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3CPC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000047051. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24082 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.8000 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) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.41500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 5000 MME, HEPES, AMMONIUM SULFATE, REMARK 280 SODIUM CHLORIDE, ISOPROPANOL, BETA-MERCAPTOETHANOL, PH 8.0, REMARK 280 VAPOR DIFFUSION, 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 33.43250 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 815 REMARK 465 HIS A 816 REMARK 465 ALA A 817 REMARK 465 GLU A 818 REMARK 465 ARG A 819 REMARK 465 GLY A 841 REMARK 465 ARG A 842 REMARK 465 GLY A 843 REMARK 465 ALA A 844 REMARK 465 PHE A 845 REMARK 465 GLY A 846 REMARK 465 GLY A 1048 REMARK 465 LEU A 1049 REMARK 465 ALA A 1050 REMARK 465 ARG A 1051 REMARK 465 ASP A 1052 REMARK 465 ILE A 1053 REMARK 465 PTR A 1054 REMARK 465 LYS A 1055 REMARK 465 ASP A 1056 REMARK 465 PRO A 1057 REMARK 465 ASP A 1058 REMARK 465 PTR A 1059 REMARK 465 VAL A 1060 REMARK 465 ARG A 1061 REMARK 465 LYS A 1062 REMARK 465 GLY A 1063 REMARK 465 ASP A 1064 REMARK 465 ALA A 1065 REMARK 465 ARG A 1066 REMARK 465 GLU B 815 REMARK 465 HIS B 816 REMARK 465 ALA B 817 REMARK 465 GLU B 818 REMARK 465 ARG B 819 REMARK 465 ARG B 842 REMARK 465 GLY B 843 REMARK 465 ALA B 844 REMARK 465 PHE B 845 REMARK 465 GLY B 846 REMARK 465 LYS B 871 REMARK 465 GLU B 872 REMARK 465 GLY B 873 REMARK 465 VAL B 990 REMARK 465 ALA B 991 REMARK 465 PRO B 992 REMARK 465 GLU B 993 REMARK 465 ASP B 994 REMARK 465 LEU B 995 REMARK 465 TYR B 996 REMARK 465 LYS B 997 REMARK 465 LEU B 1049 REMARK 465 ALA B 1050 REMARK 465 ARG B 1051 REMARK 465 ASP B 1052 REMARK 465 ILE B 1053 REMARK 465 PTR B 1054 REMARK 465 LYS B 1055 REMARK 465 ASP B 1056 REMARK 465 PRO B 1057 REMARK 465 ASP B 1058 REMARK 465 PTR B 1059 REMARK 465 VAL B 1060 REMARK 465 ARG B 1061 REMARK 465 LYS B 1062 REMARK 465 GLY B 1063 REMARK 465 ASP B 1064 REMARK 465 ALA B 1065 REMARK 465 ARG B 1066 REMARK 465 ALA B 1166 REMARK 465 ASN B 1167 REMARK 465 ALA B 1168 REMARK 465 GLN B 1169 REMARK 465 GLN B 1170 REMARK 465 ASP B 1171 REMARK 465 ARG B 1172 REMARK 465 HIS B 1173 REMARK 465 HIS B 1174 REMARK 465 HIS B 1175 REMARK 465 HIS B 1176 REMARK 465 HIS B 1177 REMARK 465 HIS B 1178 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 A1027 -21.68 79.03 REMARK 500 ASP A1112 -156.61 -118.69 REMARK 500 ARG B1027 -16.54 80.70 REMARK 500 ASP B1028 51.32 -146.49 REMARK 500 SER B1037 -168.62 -104.47 REMARK 500 TYR B1106 71.39 41.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 TYR1054 AND TYR1059 WERE PHOSPHORYLATED BY AN AUTOPHOSPHORYLATION REMARK 600 REACTION RUN ON THE PROTEIN PRIOR TO CRYSTALLIZATION. THE REMARK 600 PHOSPHORYLATED TYR IS REPRESENTED BY PTR, PHOSPHONOTYROSINE, REMARK 600 PTR1054 AND PTR1059. THESE RESIDUES ARE PART OF THE KINASE REMARK 600 ACTIVATION LOOP AND THEY ARE DISORDERED IN THE STRUCTURE AND REMARK 600 CONSEQUENTLY NOT SEEN IN THE ELECTRON DENSITY. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C52 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE C52 B 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CP9 RELATED DB: PDB REMARK 900 RELATED ID: 3CPB RELATED DB: PDB DBREF 3CPC A 815 939 UNP P35968 VGFR2_HUMAN 815 939 DBREF 3CPC A 990 1171 UNP P35968 VGFR2_HUMAN 990 1171 DBREF 3CPC B 815 939 UNP P35968 VGFR2_HUMAN 815 939 DBREF 3CPC B 990 1171 UNP P35968 VGFR2_HUMAN 990 1171 SEQADV 3CPC ALA A 817 UNP P35968 CYS 817 ENGINEERED MUTATION SEQADV 3CPC THR A 916 UNP P35968 VAL 916 ENGINEERED MUTATION SEQADV 3CPC VAL A 990 UNP P35968 GLU 990 ENGINEERED MUTATION SEQADV 3CPC ARG A 1172 UNP P35968 EXPRESSION TAG SEQADV 3CPC HIS A 1173 UNP P35968 EXPRESSION TAG SEQADV 3CPC HIS A 1174 UNP P35968 EXPRESSION TAG SEQADV 3CPC HIS A 1175 UNP P35968 EXPRESSION TAG SEQADV 3CPC HIS A 1176 UNP P35968 EXPRESSION TAG SEQADV 3CPC HIS A 1177 UNP P35968 EXPRESSION TAG SEQADV 3CPC HIS A 1178 UNP P35968 EXPRESSION TAG SEQADV 3CPC ALA B 817 UNP P35968 CYS 817 ENGINEERED MUTATION SEQADV 3CPC THR B 916 UNP P35968 VAL 916 ENGINEERED MUTATION SEQADV 3CPC VAL B 990 UNP P35968 GLU 990 ENGINEERED MUTATION SEQADV 3CPC ARG B 1172 UNP P35968 EXPRESSION TAG SEQADV 3CPC HIS B 1173 UNP P35968 EXPRESSION TAG SEQADV 3CPC HIS B 1174 UNP P35968 EXPRESSION TAG SEQADV 3CPC HIS B 1175 UNP P35968 EXPRESSION TAG SEQADV 3CPC HIS B 1176 UNP P35968 EXPRESSION TAG SEQADV 3CPC HIS B 1177 UNP P35968 EXPRESSION TAG SEQADV 3CPC HIS B 1178 UNP P35968 EXPRESSION TAG SEQRES 1 A 314 GLU HIS ALA GLU ARG LEU PRO TYR ASP ALA SER LYS TRP SEQRES 2 A 314 GLU PHE PRO ARG ASP ARG LEU LYS LEU GLY LYS PRO LEU SEQRES 3 A 314 GLY ARG GLY ALA PHE GLY GLN VAL ILE GLU ALA ASP ALA SEQRES 4 A 314 PHE GLY ILE ASP LYS THR ALA THR CYS ARG THR VAL ALA SEQRES 5 A 314 VAL LYS MET LEU LYS GLU GLY ALA THR HIS SER GLU HIS SEQRES 6 A 314 ARG ALA LEU MET SER GLU LEU LYS ILE LEU ILE HIS ILE SEQRES 7 A 314 GLY HIS HIS LEU ASN VAL VAL ASN LEU LEU GLY ALA CYS SEQRES 8 A 314 THR LYS PRO GLY GLY PRO LEU MET VAL ILE THR GLU PHE SEQRES 9 A 314 CYS LYS PHE GLY ASN LEU SER THR TYR LEU ARG SER LYS SEQRES 10 A 314 ARG ASN GLU PHE VAL PRO TYR LYS VAL ALA PRO GLU ASP SEQRES 11 A 314 LEU TYR LYS ASP PHE LEU THR LEU GLU HIS LEU ILE CYS SEQRES 12 A 314 TYR SER PHE GLN VAL ALA LYS GLY MET GLU PHE LEU ALA SEQRES 13 A 314 SER ARG LYS CYS ILE HIS ARG ASP LEU ALA ALA ARG ASN SEQRES 14 A 314 ILE LEU LEU SER GLU LYS ASN VAL VAL LYS ILE CYS ASP SEQRES 15 A 314 PHE GLY LEU ALA ARG ASP ILE PTR LYS ASP PRO ASP PTR SEQRES 16 A 314 VAL ARG LYS GLY ASP ALA ARG LEU PRO LEU LYS TRP MET SEQRES 17 A 314 ALA PRO GLU THR ILE PHE ASP ARG VAL TYR THR ILE GLN SEQRES 18 A 314 SER ASP VAL TRP SER PHE GLY VAL LEU LEU TRP GLU ILE SEQRES 19 A 314 PHE SER LEU GLY ALA SER PRO TYR PRO GLY VAL LYS ILE SEQRES 20 A 314 ASP GLU GLU PHE CYS ARG ARG LEU LYS GLU GLY THR ARG SEQRES 21 A 314 MET ARG ALA PRO ASP TYR THR THR PRO GLU MET TYR GLN SEQRES 22 A 314 THR MET LEU ASP CYS TRP HIS GLY GLU PRO SER GLN ARG SEQRES 23 A 314 PRO THR PHE SER GLU LEU VAL GLU HIS LEU GLY ASN LEU SEQRES 24 A 314 LEU GLN ALA ASN ALA GLN GLN ASP ARG HIS HIS HIS HIS SEQRES 25 A 314 HIS HIS SEQRES 1 B 314 GLU HIS ALA GLU ARG LEU PRO TYR ASP ALA SER LYS TRP SEQRES 2 B 314 GLU PHE PRO ARG ASP ARG LEU LYS LEU GLY LYS PRO LEU SEQRES 3 B 314 GLY ARG GLY ALA PHE GLY GLN VAL ILE GLU ALA ASP ALA SEQRES 4 B 314 PHE GLY ILE ASP LYS THR ALA THR CYS ARG THR VAL ALA SEQRES 5 B 314 VAL LYS MET LEU LYS GLU GLY ALA THR HIS SER GLU HIS SEQRES 6 B 314 ARG ALA LEU MET SER GLU LEU LYS ILE LEU ILE HIS ILE SEQRES 7 B 314 GLY HIS HIS LEU ASN VAL VAL ASN LEU LEU GLY ALA CYS SEQRES 8 B 314 THR LYS PRO GLY GLY PRO LEU MET VAL ILE THR GLU PHE SEQRES 9 B 314 CYS LYS PHE GLY ASN LEU SER THR TYR LEU ARG SER LYS SEQRES 10 B 314 ARG ASN GLU PHE VAL PRO TYR LYS VAL ALA PRO GLU ASP SEQRES 11 B 314 LEU TYR LYS ASP PHE LEU THR LEU GLU HIS LEU ILE CYS SEQRES 12 B 314 TYR SER PHE GLN VAL ALA LYS GLY MET GLU PHE LEU ALA SEQRES 13 B 314 SER ARG LYS CYS ILE HIS ARG ASP LEU ALA ALA ARG ASN SEQRES 14 B 314 ILE LEU LEU SER GLU LYS ASN VAL VAL LYS ILE CYS ASP SEQRES 15 B 314 PHE GLY LEU ALA ARG ASP ILE PTR LYS ASP PRO ASP PTR SEQRES 16 B 314 VAL ARG LYS GLY ASP ALA ARG LEU PRO LEU LYS TRP MET SEQRES 17 B 314 ALA PRO GLU THR ILE PHE ASP ARG VAL TYR THR ILE GLN SEQRES 18 B 314 SER ASP VAL TRP SER PHE GLY VAL LEU LEU TRP GLU ILE SEQRES 19 B 314 PHE SER LEU GLY ALA SER PRO TYR PRO GLY VAL LYS ILE SEQRES 20 B 314 ASP GLU GLU PHE CYS ARG ARG LEU LYS GLU GLY THR ARG SEQRES 21 B 314 MET ARG ALA PRO ASP TYR THR THR PRO GLU MET TYR GLN SEQRES 22 B 314 THR MET LEU ASP CYS TRP HIS GLY GLU PRO SER GLN ARG SEQRES 23 B 314 PRO THR PHE SER GLU LEU VAL GLU HIS LEU GLY ASN LEU SEQRES 24 B 314 LEU GLN ALA ASN ALA GLN GLN ASP ARG HIS HIS HIS HIS SEQRES 25 B 314 HIS HIS HET C52 A 1 29 HET C52 B 2 29 HETNAM C52 3-(2-AMINOQUINAZOLIN-6-YL)-4-METHYL-1-[3- HETNAM 2 C52 (TRIFLUOROMETHYL)PHENYL]PYRIDIN-2(1H)-ONE FORMUL 3 C52 2(C21 H15 F3 N4 O) FORMUL 5 HOH *113(H2 O) HELIX 1 1 ASP A 823 GLU A 828 1 6 HELIX 2 2 PRO A 830 ASP A 832 5 3 HELIX 3 3 THR A 875 GLY A 893 1 19 HELIX 4 4 ASN A 923 SER A 930 1 8 HELIX 5 5 PRO A 992 LYS A 997 5 6 HELIX 6 6 THR A 1001 ARG A 1022 1 22 HELIX 7 7 ALA A 1030 ARG A 1032 5 3 HELIX 8 8 GLU A 1038 ASN A 1040 5 3 HELIX 9 9 LEU A 1067 MET A 1072 5 6 HELIX 10 10 ALA A 1073 ARG A 1080 1 8 HELIX 11 11 THR A 1083 PHE A 1099 1 17 HELIX 12 12 ASP A 1112 GLU A 1121 1 10 HELIX 13 13 THR A 1132 TRP A 1143 1 12 HELIX 14 14 GLU A 1146 ARG A 1150 5 5 HELIX 15 15 THR A 1152 HIS A 1178 1 27 HELIX 16 16 ASP B 823 GLU B 828 1 6 HELIX 17 17 PRO B 830 ASP B 832 5 3 HELIX 18 18 THR B 875 GLY B 893 1 19 HELIX 19 19 ASN B 923 LYS B 931 1 9 HELIX 20 20 LEU B 1002 ARG B 1022 1 21 HELIX 21 21 ALA B 1030 ARG B 1032 5 3 HELIX 22 22 LEU B 1067 MET B 1072 5 6 HELIX 23 23 ALA B 1073 ARG B 1080 1 8 HELIX 24 24 THR B 1083 PHE B 1099 1 17 HELIX 25 25 ASP B 1112 GLY B 1122 1 11 HELIX 26 26 THR B 1132 TRP B 1143 1 12 HELIX 27 27 GLU B 1146 ARG B 1150 5 5 HELIX 28 28 THR B 1152 LEU B 1164 1 13 SHEET 1 A 5 LEU A 834 PRO A 839 0 SHEET 2 A 5 VAL A 848 PHE A 854 -1 O GLU A 850 N GLY A 837 SHEET 3 A 5 CYS A 862 MET A 869 -1 O VAL A 865 N ALA A 851 SHEET 4 A 5 MET A 913 GLU A 917 -1 O THR A 916 N ALA A 866 SHEET 5 A 5 LEU A 901 CYS A 905 -1 N LEU A 902 O ILE A 915 SHEET 1 B 2 ILE A1034 LEU A1036 0 SHEET 2 B 2 VAL A1042 ILE A1044 -1 O LYS A1043 N LEU A1035 SHEET 1 C 5 LEU B 834 PRO B 839 0 SHEET 2 C 5 VAL B 848 PHE B 854 -1 O ASP B 852 N LYS B 835 SHEET 3 C 5 CYS B 862 MET B 869 -1 O ARG B 863 N ALA B 853 SHEET 4 C 5 MET B 913 GLU B 917 -1 O THR B 916 N ALA B 866 SHEET 5 C 5 LEU B 901 CYS B 905 -1 N LEU B 902 O ILE B 915 SHEET 1 D 2 PHE B 935 VAL B 936 0 SHEET 2 D 2 LEU B1000 THR B1001 1 O LEU B1000 N VAL B 936 SHEET 1 E 2 ILE B1034 LEU B1036 0 SHEET 2 E 2 VAL B1042 ILE B1044 -1 O LYS B1043 N LEU B1035 CISPEP 1 ALA A 991 PRO A 992 0 -1.66 SITE 1 AC1 12 ALA A 866 GLU A 885 LEU A 889 THR A 916 SITE 2 AC1 12 GLU A 917 CYS A 919 HIS A1026 LEU A1035 SITE 3 AC1 12 ILE A1044 CYS A1045 ASP A1046 PHE A1047 SITE 1 AC2 12 ALA B 866 LYS B 868 GLU B 885 THR B 916 SITE 2 AC2 12 GLU B 917 PHE B 918 CYS B 919 HIS B1026 SITE 3 AC2 12 LEU B1035 ILE B1044 CYS B1045 ASP B1046 CRYST1 55.361 66.865 89.858 90.00 93.35 90.00 P 1 21 1 4 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 0.018100 0.000000 0.001100 0.00000 SCALE2 0.000000 0.015000 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011100 0.00000