PDB Short entry for 4AG8 HEADER TRANSFERASE 24-JAN-12 4AG8 TITLE CRYSTAL STRUCTURE OF THE VEGFR2 KINASE DOMAIN IN COMPLEX WITH AXITINIB TITLE 2 (AG-013736) (N-METHYL-2-(3-((E)-2-PYRIDIN-2-YL-VINYL)-1H- INDAZOL-6- TITLE 3 YLSULFANYL)-BENZAMIDE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN, RESIDUES 806-940,990-1171; COMPND 5 SYNONYM: VEGFR-2, FETAL LIVER KINASE 1, FLK-1, KINASE INSERT DOMAIN COMPND 6 RECEPTOR, KDR, PROTEIN-TYROSINE KINASE RECEPTOR FLK-1, CD309; 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 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PACSG2 KEYWDS TRANSFERASE, ANGIOGENESIS, NUCLEOTIDE-BINDING, INHIBITOR, KEYWDS 2 PHOSPHORYLATION, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR M.MCTIGUE,J.WICKERSHAM,C.PINKO,R.S.KANIA,S.BENDER REVDAT 5 20-DEC-23 4AG8 1 REMARK REVDAT 4 08-MAY-19 4AG8 1 REMARK REVDAT 3 28-JUN-17 4AG8 1 REMARK REVDAT 2 14-NOV-12 4AG8 1 JRNL REMARK DBREF REVDAT 1 26-SEP-12 4AG8 0 JRNL AUTH M.MCTIGUE,B.W.MURRAY,J.H.CHEN,Y.DENG,J.SOLOWIEJ,R.S.KANIA JRNL TITL MOLECULAR CONFORMATIONS, INTERACTIONS, AND PROPERTIES JRNL TITL 2 ASSOCIATED WITH DRUG EFFICIENCY AND CLINICAL PERFORMANCE JRNL TITL 3 AMONG VEGFR TK INHIBITORS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 18281 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22988103 JRNL DOI 10.1073/PNAS.1207759109 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 27105 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1450 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1874 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1920 REMARK 3 BIN FREE R VALUE SET COUNT : 98 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2381 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 326 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.21000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.34000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.160 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.153 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.090 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.010 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2471 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3337 ; 1.104 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 294 ; 5.439 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 355 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1872 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1171 ; 0.187 ; 0.200 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): 264 ; 0.137 ; 0.200 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): 38 ; 0.199 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.136 ; 0.200 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): 1473 ; 0.580 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2373 ; 1.133 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 998 ; 1.671 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 964 ; 2.818 ; 4.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4AG8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1290050948. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-99 REMARK 200 TEMPERATURE (KELVIN) : 87 REMARK 200 PH : 7.5 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 : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28556 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1VR2 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN AT 4 OR 13 C BY REMARK 280 THE HANGING DROP VAPOR DIFFUSION BY MIXING 2 MICORLITERS OF REMARK 280 PROTEIN-INHIBITOR COMPLEX SOLUTION WITH 2 MICROLITERS OF MOTHER REMARK 280 LIQUOR (100 MM HEPES (PH 7.5), 200 MM AMMONIUM SULFATE, 5% (V/V) REMARK 280 MPD, AND 15-20% (W/V) POLYETHYLENE GLYCOL (MW = 6000)). BEFORE REMARK 280 SEALING THE COVERSLIPS ABOVE THE RESERVOIRS, BETA- REMARK 280 MERCAPTOETHANOL WAS ADDED TO THE RESERVOIRS TO A FINAL REMARK 280 CONCENTRATION OF 60 MM. THIS PROCEDURE PRODUCED MICROCRYSTALS REMARK 280 THAT WERE SUBSEQUENTLY USED TO SEED MORE CRYSTALLIZATION DROPS REMARK 280 AFTER 12-18 HOURS OF EQUILIBRATION., VAPOR DIFFUSION, HANGING REMARK 280 DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 67.83000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.61050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.83000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.61050 REMARK 290 SMTRY3 4 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLU 990 TO VAL 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 MET A 806 REMARK 465 ASP A 807 REMARK 465 PRO A 808 REMARK 465 ASP A 809 REMARK 465 GLU A 810 REMARK 465 LEU A 811 REMARK 465 PRO A 812 REMARK 465 LEU A 813 REMARK 465 ASP A 814 REMARK 465 GLU A 815 REMARK 465 LYS A 939 REMARK 465 VAL A 990 REMARK 465 ALA A 991 REMARK 465 PRO A 992 REMARK 465 GLU A 993 REMARK 465 ASP A 994 REMARK 465 LEU A 995 REMARK 465 GLN A 1169 REMARK 465 GLN A 1170 REMARK 465 ASP A 1171 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 A1028 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A1058 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A1087 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A1141 CB - CG - OD1 ANGL. DEV. = 5.4 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 -12.60 76.08 REMARK 500 ASP A1028 45.92 -140.91 REMARK 500 SER A1037 -168.12 -107.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2048 DISTANCE = 6.38 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AXI A 2000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y6A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VEGFR2 IN COMPLEX WITH A 2- ANILINO-5-ARYL- REMARK 900 OXAZOLE INHIBITOR REMARK 900 RELATED ID: 2X1W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH DOMAINS 2 AND 3 OF REMARK 900 VEGFR2 REMARK 900 RELATED ID: 1Y6B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VEGFR2 IN COMPLEX WITH A 2- ANILINO-5-ARYL- REMARK 900 OXAZOLE INHIBITOR REMARK 900 RELATED ID: 2X1X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH DOMAINS 2 AND 3 OF REMARK 900 VEGFR2 IN A TETRAGONAL CRYSTAL FORM REMARK 900 RELATED ID: 2XIR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE VEGFR2 KINASE DOMAIN IN COMPLEX WITH PF- REMARK 900 00337210 (N,2-DIMETHYL-6-(7-(2- MORPHOLINOETHOXY)QUINOLIN-4-YLOXY) REMARK 900 BENZOFURAN-3-CARBOXAMIDE) REMARK 900 RELATED ID: 1YWN RELATED DB: PDB REMARK 900 VEGFR2 IN COMPLEX WITH A NOVEL 4-AMINO-FURO[2,3-D] PYRIMIDINE REMARK 900 RELATED ID: 1VR2 RELATED DB: PDB REMARK 900 HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2 (KDR) KINASE REMARK 900 DOMAIN REMARK 900 RELATED ID: 4AGC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VEGFR2 (JUXTAMEMBRANE AND KINASE DOMAINS) IN REMARK 900 COMPLEX WITH AXITINIB (AG-013736) (N- METHYL-2-(3-((E)-2-PYRIDIN-2- REMARK 900 YL-VINYL)-1H-INDAZOL -6-YLSULFANYL)-BENZAMIDE) REMARK 900 RELATED ID: 4AGD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VEGFR2 (JUXTAMEMBRANE AND KINASE DOMAINS) IN REMARK 900 COMPLEX WITH SUNITINIB (SU11248) (N-2- DIETHYLAMINOETHYL)-5-((Z)-(5- REMARK 900 FLUORO-2-OXO-1H-INDOL-3 -YLIDENE)METHYL)-2,4-DIMETHYL-1H-PYRROLE-3- REMARK 900 CARBOXAMIDE) REMARK 900 RELATED ID: 4ASD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VEGFR2 (JUXTAMEMBRANE AND KINASE DOMAINS) IN REMARK 900 COMPLEX WITH SORAFENIB (BAY 43-9006) REMARK 900 RELATED ID: 4ASE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VEGFR2 (JUXTAMEMBRANE AND KINASE DOMAINS) IN REMARK 900 COMPLEX WITH TIVOZANIB (AV-951) DBREF 4AG8 A 806 939 UNP P35968 VGFR2_HUMAN 806 939 DBREF 4AG8 A 990 1171 UNP P35968 VGFR2_HUMAN 990 1171 SEQADV 4AG8 VAL A 990 UNP P35968 GLU 990 ENGINEERED MUTATION SEQRES 1 A 316 MET ASP PRO ASP GLU LEU PRO LEU ASP GLU HIS CYS GLU SEQRES 2 A 316 ARG LEU PRO TYR ASP ALA SER LYS TRP GLU PHE PRO ARG SEQRES 3 A 316 ASP ARG LEU LYS LEU GLY LYS PRO LEU GLY ARG GLY ALA SEQRES 4 A 316 PHE GLY GLN VAL ILE GLU ALA ASP ALA PHE GLY ILE ASP SEQRES 5 A 316 LYS THR ALA THR CYS ARG THR VAL ALA VAL LYS MET LEU SEQRES 6 A 316 LYS GLU GLY ALA THR HIS SER GLU HIS ARG ALA LEU MET SEQRES 7 A 316 SER GLU LEU LYS ILE LEU ILE HIS ILE GLY HIS HIS LEU SEQRES 8 A 316 ASN VAL VAL ASN LEU LEU GLY ALA CYS THR LYS PRO GLY SEQRES 9 A 316 GLY PRO LEU MET VAL ILE VAL GLU PHE CYS LYS PHE GLY SEQRES 10 A 316 ASN LEU SER THR TYR LEU ARG SER LYS ARG ASN GLU PHE SEQRES 11 A 316 VAL PRO TYR LYS VAL ALA PRO GLU ASP LEU TYR LYS ASP SEQRES 12 A 316 PHE LEU THR LEU GLU HIS LEU ILE CYS TYR SER PHE GLN SEQRES 13 A 316 VAL ALA LYS GLY MET GLU PHE LEU ALA SER ARG LYS CYS SEQRES 14 A 316 ILE HIS ARG ASP LEU ALA ALA ARG ASN ILE LEU LEU SER SEQRES 15 A 316 GLU LYS ASN VAL VAL LYS ILE CYS ASP PHE GLY LEU ALA SEQRES 16 A 316 ARG ASP ILE TYR LYS ASP PRO ASP TYR VAL ARG LYS GLY SEQRES 17 A 316 ASP ALA ARG LEU PRO LEU LYS TRP MET ALA PRO GLU THR SEQRES 18 A 316 ILE PHE ASP ARG VAL TYR THR ILE GLN SER ASP VAL TRP SEQRES 19 A 316 SER PHE GLY VAL LEU LEU TRP GLU ILE PHE SER LEU GLY SEQRES 20 A 316 ALA SER PRO TYR PRO GLY VAL LYS ILE ASP GLU GLU PHE SEQRES 21 A 316 CYS ARG ARG LEU LYS GLU GLY THR ARG MET ARG ALA PRO SEQRES 22 A 316 ASP TYR THR THR PRO GLU MET TYR GLN THR MET LEU ASP SEQRES 23 A 316 CYS TRP HIS GLY GLU PRO SER GLN ARG PRO THR PHE SER SEQRES 24 A 316 GLU LEU VAL GLU HIS LEU GLY ASN LEU LEU GLN ALA ASN SEQRES 25 A 316 ALA GLN GLN ASP HET AXI A2000 28 HETNAM AXI AXITINIB HETSYN AXI N-METHYL-2-(3-((E)-2-PYRIDIN-2-YL-VINYL)-1H-INDAZOL-6- HETSYN 2 AXI YLSULFANYL)-BENZAMIDE FORMUL 2 AXI C22 H18 N4 O S FORMUL 3 HOH *326(H2 O) HELIX 1 1 HIS A 816 LEU A 820 5 5 HELIX 2 2 ASP A 823 GLU A 828 1 6 HELIX 3 3 PRO A 830 ASP A 832 5 3 HELIX 4 4 THR A 875 GLY A 893 1 19 HELIX 5 5 LEU A 924 SER A 930 1 7 HELIX 6 6 LEU A 1002 ARG A 1022 1 21 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 PHE A 1047 ARG A 1051 5 5 HELIX 10 10 PRO A 1068 MET A 1072 5 5 HELIX 11 11 ALA A 1073 ARG A 1080 1 8 HELIX 12 12 THR A 1083 SER A 1100 1 18 HELIX 13 13 ASP A 1112 GLY A 1122 1 11 HELIX 14 14 THR A 1132 TRP A 1143 1 12 HELIX 15 15 GLU A 1146 ARG A 1150 5 5 HELIX 16 16 THR A 1152 ALA A 1168 1 17 SHEET 1 AA 5 LEU A 834 ARG A 842 0 SHEET 2 AA 5 GLY A 846 PHE A 854 -1 O VAL A 848 N LEU A 840 SHEET 3 AA 5 CYS A 862 LEU A 870 -1 O ARG A 863 N ALA A 853 SHEET 4 AA 5 MET A 913 GLU A 917 -1 O VAL A 914 N LYS A 868 SHEET 5 AA 5 LEU A 901 CYS A 905 -1 N LEU A 902 O ILE A 915 SHEET 1 AB 3 GLY A 922 ASN A 923 0 SHEET 2 AB 3 ILE A1034 LEU A1036 -1 N LEU A1036 O GLY A 922 SHEET 3 AB 3 VAL A1042 ILE A1044 -1 O LYS A1043 N LEU A1035 SHEET 1 AC 2 PHE A 935 VAL A 936 0 SHEET 2 AC 2 LEU A1000 THR A1001 1 O LEU A1000 N VAL A 936 SHEET 1 AD 2 VAL A1060 LYS A1062 0 SHEET 2 AD 2 ALA A1065 LEU A1067 -1 O ALA A1065 N LYS A1062 SITE 1 AC1 17 VAL A 848 ALA A 866 LYS A 868 GLU A 885 SITE 2 AC1 17 VAL A 899 VAL A 914 VAL A 916 GLU A 917 SITE 3 AC1 17 PHE A 918 CYS A 919 LYS A 920 GLY A 922 SITE 4 AC1 17 LEU A1035 CYS A1045 ASP A1046 PHE A1047 SITE 5 AC1 17 HOH A2085 CRYST1 135.660 57.221 51.829 90.00 93.44 90.00 C 1 2 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 0.007371 0.000000 0.000443 0.00000 SCALE2 0.000000 0.017476 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019329 0.00000