HEADER TRANSFERASE/TRANSFERASE INHIBITOR 24-SEP-14 3WZD TITLE KDR IN COMPLEX WITH LIGAND LENVATINIB COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN (UNP RESIDUES 814-940, 991-1172); COMPND 5 SYNONYM: VEGFR-2, FETAL LIVER KINASE 1, FLK-1, KINASE INSERT DOMAIN COMPND 6 RECEPTOR, KDR, PROTEIN-TYROSINE KINASE RECEPTOR FLK-1; 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, VEGFR2; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS KDR RECEPTOR KINASE, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.OKAMOTO,M.IKEMORI_KAWADA,A.INOUE,J.MATSUI REVDAT 1 27-MAY-15 3WZD 0 JRNL AUTH K.OKAMOTO,M.IKEMORI-KAWADA,A.JESTEL,K.VON KONIG,Y.FUNAHASHI, JRNL AUTH 2 T.MATSUSHIMA,A.TSURUOKA,A.INOUE,J.MATSUI JRNL TITL DISTINCT BINDING MODE OF MULTIKINASE INHIBITOR LENVATINIB JRNL TITL 2 REVEALED BY BIOCHEMICAL CHARACTERIZATION. JRNL REF ACS MED.CHEM.LETT. V. 6 89 2015 JRNL REFN ISSN 1948-5875 JRNL PMID 25589937 JRNL DOI 10.1021/ML500394M REMARK 2 REMARK 2 RESOLUTION. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 40823 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4082 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) : 1.57 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.61 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2945 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE SET COUNT : 323 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2224 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 89 REMARK 3 SOLVENT ATOMS : 213 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.11000 REMARK 3 B22 (A**2) : -0.51000 REMARK 3 B33 (A**2) : 0.77000 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : -1.17000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.084 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.070 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.054 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2348 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2253 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3166 ; 1.580 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5166 ; 1.027 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 283 ; 5.942 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;32.617 ;22.872 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 387 ;11.547 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;19.719 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 348 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2579 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 535 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; 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): 1129 ; 2.584 ; 2.043 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1128 ; 2.583 ; 2.041 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1413 ; 3.310 ; 3.423 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1219 ; 4.204 ; 2.507 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; 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 918 REMARK 3 ORIGIN FOR THE GROUP (A): -1.5310 -13.6480 8.2850 REMARK 3 T TENSOR REMARK 3 T11: 0.0654 T22: 0.0611 REMARK 3 T33: 0.0483 T12: 0.0125 REMARK 3 T13: 0.0028 T23: -0.0206 REMARK 3 L TENSOR REMARK 3 L11: 2.4311 L22: 2.9254 REMARK 3 L33: 2.9128 L12: 1.1723 REMARK 3 L13: 0.6436 L23: -0.4628 REMARK 3 S TENSOR REMARK 3 S11: -0.0465 S12: 0.2000 S13: -0.0791 REMARK 3 S21: -0.1045 S22: 0.0739 S23: 0.0197 REMARK 3 S31: 0.0428 S32: 0.0147 S33: -0.0275 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 : A 921 A 1167 REMARK 3 ORIGIN FOR THE GROUP (A): 13.5300 5.8360 21.7580 REMARK 3 T TENSOR REMARK 3 T11: 0.0129 T22: 0.0415 REMARK 3 T33: 0.0379 T12: -0.0117 REMARK 3 T13: 0.0103 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 1.1734 L22: 2.2429 REMARK 3 L33: 2.0631 L12: -0.3396 REMARK 3 L13: 0.2518 L23: -0.2820 REMARK 3 S TENSOR REMARK 3 S11: 0.0288 S12: 0.0514 S13: -0.0045 REMARK 3 S21: 0.0428 S22: 0.0081 S23: -0.1104 REMARK 3 S31: -0.1019 S32: 0.1211 S33: -0.0368 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3WZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-SEP-14. REMARK 100 THE RCSB ID CODE IS RCSB096983. 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 : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00003 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44907 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 46.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.44400 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: NULL 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 (%): 49.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CHES,5-20% PEG 8000, PH 9.5, 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 42.11250 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 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 ASP A 814 REMARK 465 GLU A 815 REMARK 465 HIS A 816 REMARK 465 CYS A 817 REMARK 465 GLU A 818 REMARK 465 ARG A 819 REMARK 465 ARG A 842 REMARK 465 GLY A 843 REMARK 465 ALA A 844 REMARK 465 PHE A 845 REMARK 465 ARG A 1051 REMARK 465 ASP A 1052 REMARK 465 ILE A 1053 REMARK 465 TYR A 1054 REMARK 465 LYS A 1055 REMARK 465 ASP A 1056 REMARK 465 PRO A 1057 REMARK 465 ASP A 1058 REMARK 465 TYR 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 ALA A 1168 REMARK 465 GLN A 1169 REMARK 465 GLN A 1170 REMARK 465 ASP A 1171 REMARK 465 GLY A 1172 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 847 CG CD OE1 NE2 REMARK 480 LYS A 858 CG CD CE NZ REMARK 480 LYS A 871 CE NZ REMARK 480 GLU A 872 CG CD OE1 OE2 REMARK 480 LYS A 887 CE NZ REMARK 480 LYS A 920 CE NZ REMARK 480 LYS A 1014 NZ REMARK 480 LYS A 1023 CE NZ REMARK 480 LEU A 1067 CG CD1 CD2 REMARK 480 GLU A 1121 CG CD OE1 OE2 REMARK 480 GLU A 1146 CD OE1 OE2 REMARK 480 GLN A 1165 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A1087 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A1087 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES 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 ARG A1027 -20.42 82.13 REMARK 500 ASP A1028 54.36 -145.14 REMARK 500 SER A1037 -165.87 -101.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 DTT A 1202 REMARK 615 DTT A 1203 REMARK 615 DTT A 1205 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LEV A 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTT A 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTT A 1203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTT A 1204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTT A 1205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1209 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1210 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1211 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WZE RELATED DB: PDB DBREF 3WZD A 814 1172 UNP P35968 VGFR2_HUMAN 814 1172 SEQADV 3WZD VAL A 940 UNP P35968 THR 940 ENGINEERED MUTATION SEQADV 3WZD A UNP P35968 LYS 941 DELETION SEQADV 3WZD A UNP P35968 GLY 942 DELETION SEQADV 3WZD A UNP P35968 ALA 943 DELETION SEQADV 3WZD A UNP P35968 ARG 944 DELETION SEQADV 3WZD A UNP P35968 PHE 945 DELETION SEQADV 3WZD A UNP P35968 ARG 946 DELETION SEQADV 3WZD A UNP P35968 GLN 947 DELETION SEQADV 3WZD A UNP P35968 GLY 948 DELETION SEQADV 3WZD A UNP P35968 LYS 949 DELETION SEQADV 3WZD A UNP P35968 ASP 950 DELETION SEQADV 3WZD A UNP P35968 TYR 951 DELETION SEQADV 3WZD A UNP P35968 VAL 952 DELETION SEQADV 3WZD A UNP P35968 GLY 953 DELETION SEQADV 3WZD A UNP P35968 ALA 954 DELETION SEQADV 3WZD A UNP P35968 ILE 955 DELETION SEQADV 3WZD A UNP P35968 PRO 956 DELETION SEQADV 3WZD A UNP P35968 VAL 957 DELETION SEQADV 3WZD A UNP P35968 ASP 958 DELETION SEQADV 3WZD A UNP P35968 LEU 959 DELETION SEQADV 3WZD A UNP P35968 LYS 960 DELETION SEQADV 3WZD A UNP P35968 ARG 961 DELETION SEQADV 3WZD A UNP P35968 ARG 962 DELETION SEQADV 3WZD A UNP P35968 LEU 963 DELETION SEQADV 3WZD A UNP P35968 ASP 964 DELETION SEQADV 3WZD A UNP P35968 SER 965 DELETION SEQADV 3WZD A UNP P35968 ILE 966 DELETION SEQADV 3WZD A UNP P35968 THR 967 DELETION SEQADV 3WZD A UNP P35968 SER 968 DELETION SEQADV 3WZD A UNP P35968 SER 969 DELETION SEQADV 3WZD A UNP P35968 GLN 970 DELETION SEQADV 3WZD A UNP P35968 SER 971 DELETION SEQADV 3WZD A UNP P35968 SER 972 DELETION SEQADV 3WZD A UNP P35968 ALA 973 DELETION SEQADV 3WZD A UNP P35968 SER 974 DELETION SEQADV 3WZD A UNP P35968 SER 975 DELETION SEQADV 3WZD A UNP P35968 GLY 976 DELETION SEQADV 3WZD A UNP P35968 PHE 977 DELETION SEQADV 3WZD A UNP P35968 VAL 978 DELETION SEQADV 3WZD A UNP P35968 GLU 979 DELETION SEQADV 3WZD A UNP P35968 GLU 980 DELETION SEQADV 3WZD A UNP P35968 LYS 981 DELETION SEQADV 3WZD A UNP P35968 SER 982 DELETION SEQADV 3WZD A UNP P35968 LEU 983 DELETION SEQADV 3WZD A UNP P35968 SER 984 DELETION SEQADV 3WZD A UNP P35968 ASP 985 DELETION SEQADV 3WZD A UNP P35968 GLU 987 DELETION SEQADV 3WZD A UNP P35968 GLU 988 DELETION SEQADV 3WZD A UNP P35968 GLU 989 DELETION SEQADV 3WZD A UNP P35968 GLU 990 DELETION SEQRES 1 A 309 ASP GLU HIS CYS GLU ARG LEU PRO TYR ASP ALA SER LYS SEQRES 2 A 309 TRP GLU PHE PRO ARG ASP ARG LEU LYS LEU GLY LYS PRO SEQRES 3 A 309 LEU GLY ARG GLY ALA PHE GLY GLN VAL ILE GLU ALA ASP SEQRES 4 A 309 ALA PHE GLY ILE ASP LYS THR ALA THR CYS ARG THR VAL SEQRES 5 A 309 ALA VAL LYS MET LEU LYS GLU GLY ALA THR HIS SER GLU SEQRES 6 A 309 HIS ARG ALA LEU MET SER GLU LEU LYS ILE LEU ILE HIS SEQRES 7 A 309 ILE GLY HIS HIS LEU ASN VAL VAL ASN LEU LEU GLY ALA SEQRES 8 A 309 CYS THR LYS PRO GLY GLY PRO LEU MET VAL ILE VAL GLU SEQRES 9 A 309 PHE CYS LYS PHE GLY ASN LEU SER THR TYR LEU ARG SER SEQRES 10 A 309 LYS ARG ASN GLU PHE VAL PRO TYR LYS VAL ALA PRO GLU SEQRES 11 A 309 ASP LEU TYR LYS ASP PHE LEU THR LEU GLU HIS LEU ILE SEQRES 12 A 309 CYS TYR SER PHE GLN VAL ALA LYS GLY MET GLU PHE LEU SEQRES 13 A 309 ALA SER ARG LYS CYS ILE HIS ARG ASP LEU ALA ALA ARG SEQRES 14 A 309 ASN ILE LEU LEU SER GLU LYS ASN VAL VAL LYS ILE CYS SEQRES 15 A 309 ASP PHE GLY LEU ALA ARG ASP ILE TYR LYS ASP PRO ASP SEQRES 16 A 309 TYR VAL ARG LYS GLY ASP ALA ARG LEU PRO LEU LYS TRP SEQRES 17 A 309 MET ALA PRO GLU THR ILE PHE ASP ARG VAL TYR THR ILE SEQRES 18 A 309 GLN SER ASP VAL TRP SER PHE GLY VAL LEU LEU TRP GLU SEQRES 19 A 309 ILE PHE SER LEU GLY ALA SER PRO TYR PRO GLY VAL LYS SEQRES 20 A 309 ILE ASP GLU GLU PHE CYS ARG ARG LEU LYS GLU GLY THR SEQRES 21 A 309 ARG MET ARG ALA PRO ASP TYR THR THR PRO GLU MET TYR SEQRES 22 A 309 GLN THR MET LEU ASP CYS TRP HIS GLY GLU PRO SER GLN SEQRES 23 A 309 ARG PRO THR PHE SER GLU LEU VAL GLU HIS LEU GLY ASN SEQRES 24 A 309 LEU LEU GLN ALA ASN ALA GLN GLN ASP GLY HET LEV A1201 30 HET DTT A1202 8 HET DTT A1203 8 HET DTT A1204 8 HET DTT A1205 8 HET EDO A1206 4 HET EDO A1207 4 HET EDO A1208 4 HET EDO A1209 4 HET GOL A1210 6 HET SO4 A1211 5 HETNAM LEV 4-{3-CHLORO-4-[(CYCLOPROPYLCARBAMOYL)AMINO]PHENOXY}-7- HETNAM 2 LEV METHOXYQUINOLINE-6-CARBOXAMIDE HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN LEV LENVATINIB HETSYN DTT 1,4-DITHIOTHREITOL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 LEV C21 H19 CL N4 O4 FORMUL 3 DTT 4(C4 H10 O2 S2) FORMUL 7 EDO 4(C2 H6 O2) FORMUL 11 GOL C3 H8 O3 FORMUL 12 SO4 O4 S 2- FORMUL 13 HOH *213(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 LEU A 924 LYS A 931 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 SER A 1100 1 18 HELIX 12 12 ASP A 1112 GLY A 1122 1 11 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 ASN A 1167 1 16 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 LYS A 838 SHEET 3 A 5 CYS A 862 MET A 869 -1 O ARG A 863 N ALA A 853 SHEET 4 A 5 MET A 913 GLU A 917 -1 O VAL 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 3 GLY A 922 ASN A 923 0 SHEET 2 B 3 ILE A1034 LEU A1036 -1 O LEU A1036 N GLY A 922 SHEET 3 B 3 VAL A1042 ILE A1044 -1 O LYS A1043 N LEU A1035 LINK SG CYS A 862 S4 DTT A1203 1555 1555 2.04 LINK SG CYS A1007 S4 DTT A1205 1555 1555 1.97 LINK SG CYS A1024 S4 DTT A1202 1555 1555 2.03 LINK SG CYS A1116 S4 DTT A1204 1555 1555 2.05 CISPEP 1 ALA A 991 PRO A 992 0 -2.86 SITE 1 AC1 18 GLY A 841 ALA A 866 GLU A 885 ILE A 888 SITE 2 AC1 18 VAL A 899 GLU A 917 PHE A 918 CYS A 919 SITE 3 AC1 18 LYS A 920 GLY A 922 LEU A1035 CYS A1045 SITE 4 AC1 18 ASP A1046 PHE A1047 GOL A1210 HOH A3001 SITE 5 AC1 18 HOH A3002 HOH A3003 SITE 1 AC2 2 CYS A1024 ILE A1025 SITE 1 AC3 4 ASP A 852 CYS A 862 ARG A 863 THR A 864 SITE 1 AC4 5 ILE A1077 PHE A1078 ASP A1112 GLU A1113 SITE 2 AC4 5 CYS A1116 SITE 1 AC5 2 CYS A1007 LEU A1164 SITE 1 AC6 5 PHE A 921 TYR A 927 SER A 930 HOH A3014 SITE 2 AC6 5 HOH A3029 SITE 1 AC7 7 ALA A1020 ILE A1084 GLN A1085 THR A1152 SITE 2 AC7 7 PHE A1153 SER A1154 HOH A3090 SITE 1 AC8 6 TRP A1096 SER A1100 PRO A1128 ASP A1129 SITE 2 AC8 6 HOH A3129 HOH A3162 SITE 1 AC9 6 PHE A 921 SER A1037 GLU A1038 LYS A1039 SITE 2 AC9 6 ASN A1040 HOH A3082 SITE 1 BC1 7 ARG A1032 ASN A1033 CYS A1045 ASP A1046 SITE 2 BC1 7 LEV A1201 HOH A3001 HOH A3013 SITE 1 BC2 4 GLU A1003 HIS A1004 CYS A1007 ASN A1040 CRYST1 42.334 84.225 46.892 90.00 100.20 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 0.023622 0.000000 0.004250 0.00000 SCALE2 0.000000 0.011873 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021668 0.00000