PDB Short entry for 4AGC HEADER TRANSFERASE 26-JAN-12 4AGC TITLE CRYSTAL STRUCTURE OF VEGFR2 (JUXTAMEMBRANE AND KINASE DOMAINS) IN TITLE 2 COMPLEX WITH AXITINIB (AG-013736) (N-METHYL-2-(3-((E)-2-PYRIDIN-2-YL- TITLE 3 VINYL)-1H-INDAZOL-6-YLSULFANYL)-BENZAMIDE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: JUXTAMEMBRANE AND KINASE DOMAINS, RESIDUES 787-939,990- COMPND 5 1171; COMPND 6 SYNONYM: VEGFR-2, FETAL LIVER KINASE 1, FLK-1, KINASE INSERT DOMAIN COMPND 7 RECEPTOR, KDR, PROTEIN-TYROSINE KINASE RECEPTOR FLK-1, CD309; COMPND 8 EC: 2.7.10.1; COMPND 9 ENGINEERED: YES; COMPND 10 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: PFASTBAC KEYWDS TRANSFERASE, ANGIOGENESIS, NUCLEOTIDE-BINDING, INHIBITOR, KEYWDS 2 PHOSPHORYLATION, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR M.MCTIGUE,Y.DENG,K.RYAN,A.BROOUN,W.DIEHL,R.S.KANIA REVDAT 4 20-DEC-23 4AGC 1 REMARK REVDAT 3 08-MAY-19 4AGC 1 REMARK REVDAT 2 14-NOV-12 4AGC 1 JRNL REVDAT 1 26-SEP-12 4AGC 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. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2005 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 198974.170 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 24733 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.900 REMARK 3 FREE R VALUE TEST SET COUNT : 710 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3141 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 2.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 91 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2442 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.86000 REMARK 3 B22 (A**2) : -1.06000 REMARK 3 B33 (A**2) : -0.80000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.25000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.20 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.630 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.510 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.360 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.310 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.500 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 57.07 REMARK 3 REMARK 3 NCS MODEL : NONE REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : PFI.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : PFI.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4AGC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1290051068. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 87 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25951 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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 4AG8 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN AT 13 DEGREES C BY REMARK 280 THE HANGING DROP VAPOR DIFFUSION METHOD USING PRECIPITANT REMARK 280 SOLUTIONS CONTAINING: 0.2M SODIUM CITRATE (PH 6.0 -6.5) AND 14- REMARK 280 21% (W/V) POLYETHYLENE GLYCOL MW = 3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 286K 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 69.74600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.46100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 69.74600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.46100 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 769 REMARK 465 GLY A 770 REMARK 465 GLY A 771 REMARK 465 HIS A 772 REMARK 465 HIS A 773 REMARK 465 HIS A 774 REMARK 465 HIS A 775 REMARK 465 HIS A 776 REMARK 465 HIS A 777 REMARK 465 GLY A 778 REMARK 465 LEU A 779 REMARK 465 GLU A 780 REMARK 465 VAL A 781 REMARK 465 LEU A 782 REMARK 465 PHE A 783 REMARK 465 GLN A 784 REMARK 465 GLY A 785 REMARK 465 PRO A 786 REMARK 465 ARG A 787 REMARK 465 THR A 788 REMARK 465 VAL A 789 REMARK 465 LYS A 790 REMARK 465 ARG A 791 REMARK 465 ALA A 792 REMARK 465 ASN A 793 REMARK 465 GLY A 794 REMARK 465 GLY A 795 REMARK 465 GLU A 796 REMARK 465 LEU A 797 REMARK 465 LYS A 798 REMARK 465 THR A 799 REMARK 465 GLY A 800 REMARK 465 LEU A 813 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 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 1170 REMARK 465 ASP A 1171 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 GLN A1169 CA C O CB CG CD OE1 REMARK 470 GLN A1169 NE2 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 ASP A 998 -3.29 80.00 REMARK 500 ASP A1028 44.08 -145.83 REMARK 500 SER A1037 -164.53 -110.86 REMARK 500 ASP A1112 -159.92 -134.53 REMARK 500 ALA A1168 -72.50 -96.21 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 A2013 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A2150 DISTANCE = 5.96 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: 4AG8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE VEGFR2 KINASE DOMAIN IN COMPLEX WITH REMARK 900 AXITINIB (AG-013736) (N-METHYL-2-(3-((E )-2-PYRIDIN-2-YL-VINYL)-1H- REMARK 900 INDAZOL-6-YLSULFANYL)- BENZAMIDE) 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: 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) DBREF 4AGC A 787 939 UNP P35968 VGFR2_HUMAN 787 939 DBREF 4AGC A 990 1171 UNP P35968 VGFR2_HUMAN 990 1171 SEQADV 4AGC MET A 769 UNP P35968 EXPRESSION TAG SEQADV 4AGC GLY A 770 UNP P35968 EXPRESSION TAG SEQADV 4AGC GLY A 771 UNP P35968 EXPRESSION TAG SEQADV 4AGC HIS A 772 UNP P35968 EXPRESSION TAG SEQADV 4AGC HIS A 773 UNP P35968 EXPRESSION TAG SEQADV 4AGC HIS A 774 UNP P35968 EXPRESSION TAG SEQADV 4AGC HIS A 775 UNP P35968 EXPRESSION TAG SEQADV 4AGC HIS A 776 UNP P35968 EXPRESSION TAG SEQADV 4AGC HIS A 777 UNP P35968 EXPRESSION TAG SEQADV 4AGC GLY A 778 UNP P35968 EXPRESSION TAG SEQADV 4AGC LEU A 779 UNP P35968 EXPRESSION TAG SEQADV 4AGC GLU A 780 UNP P35968 EXPRESSION TAG SEQADV 4AGC VAL A 781 UNP P35968 EXPRESSION TAG SEQADV 4AGC LEU A 782 UNP P35968 EXPRESSION TAG SEQADV 4AGC PHE A 783 UNP P35968 EXPRESSION TAG SEQADV 4AGC GLN A 784 UNP P35968 EXPRESSION TAG SEQADV 4AGC GLY A 785 UNP P35968 EXPRESSION TAG SEQADV 4AGC PRO A 786 UNP P35968 EXPRESSION TAG SEQADV 4AGC VAL A 990 UNP P35968 GLU 990 ENGINEERED MUTATION SEQRES 1 A 353 MET GLY GLY HIS HIS HIS HIS HIS HIS GLY LEU GLU VAL SEQRES 2 A 353 LEU PHE GLN GLY PRO ARG THR VAL LYS ARG ALA ASN GLY SEQRES 3 A 353 GLY GLU LEU LYS THR GLY TYR LEU SER ILE VAL MET ASP SEQRES 4 A 353 PRO ASP GLU LEU PRO LEU ASP GLU HIS CYS GLU ARG LEU SEQRES 5 A 353 PRO TYR ASP ALA SER LYS TRP GLU PHE PRO ARG ASP ARG SEQRES 6 A 353 LEU LYS LEU GLY LYS PRO LEU GLY ARG GLY ALA PHE GLY SEQRES 7 A 353 GLN VAL ILE GLU ALA ASP ALA PHE GLY ILE ASP LYS THR SEQRES 8 A 353 ALA THR CYS ARG THR VAL ALA VAL LYS MET LEU LYS GLU SEQRES 9 A 353 GLY ALA THR HIS SER GLU HIS ARG ALA LEU MET SER GLU SEQRES 10 A 353 LEU LYS ILE LEU ILE HIS ILE GLY HIS HIS LEU ASN VAL SEQRES 11 A 353 VAL ASN LEU LEU GLY ALA CYS THR LYS PRO GLY GLY PRO SEQRES 12 A 353 LEU MET VAL ILE VAL GLU PHE CYS LYS PHE GLY ASN LEU SEQRES 13 A 353 SER THR TYR LEU ARG SER LYS ARG ASN GLU PHE VAL PRO SEQRES 14 A 353 TYR LYS VAL ALA PRO GLU ASP LEU TYR LYS ASP PHE LEU SEQRES 15 A 353 THR LEU GLU HIS LEU ILE CYS TYR SER PHE GLN VAL ALA SEQRES 16 A 353 LYS GLY MET GLU PHE LEU ALA SER ARG LYS CYS ILE HIS SEQRES 17 A 353 ARG ASP LEU ALA ALA ARG ASN ILE LEU LEU SER GLU LYS SEQRES 18 A 353 ASN VAL VAL LYS ILE CYS ASP PHE GLY LEU ALA ARG ASP SEQRES 19 A 353 ILE TYR LYS ASP PRO ASP TYR VAL ARG LYS GLY ASP ALA SEQRES 20 A 353 ARG LEU PRO LEU LYS TRP MET ALA PRO GLU THR ILE PHE SEQRES 21 A 353 ASP ARG VAL TYR THR ILE GLN SER ASP VAL TRP SER PHE SEQRES 22 A 353 GLY VAL LEU LEU TRP GLU ILE PHE SER LEU GLY ALA SER SEQRES 23 A 353 PRO TYR PRO GLY VAL LYS ILE ASP GLU GLU PHE CYS ARG SEQRES 24 A 353 ARG LEU LYS GLU GLY THR ARG MET ARG ALA PRO ASP TYR SEQRES 25 A 353 THR THR PRO GLU MET TYR GLN THR MET LEU ASP CYS TRP SEQRES 26 A 353 HIS GLY GLU PRO SER GLN ARG PRO THR PHE SER GLU LEU SEQRES 27 A 353 VAL GLU HIS LEU GLY ASN LEU LEU GLN ALA ASN ALA GLN SEQRES 28 A 353 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 *151(H2 O) HELIX 1 1 PRO A 808 LEU A 811 5 4 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 ASN A 923 SER A 930 1 8 HELIX 6 6 LYS A 931 GLU A 934 5 4 HELIX 7 7 THR A 1001 ARG A 1022 1 22 HELIX 8 8 ALA A 1030 ARG A 1032 5 3 HELIX 9 9 GLU A 1038 ASN A 1040 5 3 HELIX 10 10 PHE A 1047 ARG A 1051 5 5 HELIX 11 11 PRO A 1068 MET A 1072 5 5 HELIX 12 12 ALA A 1073 ARG A 1080 1 8 HELIX 13 13 THR A 1083 PHE A 1099 1 17 HELIX 14 14 ASP A 1112 GLY A 1122 1 11 HELIX 15 15 THR A 1132 TRP A 1143 1 12 HELIX 16 16 GLU A 1146 ARG A 1150 5 5 HELIX 17 17 THR A 1152 ASN A 1167 1 16 SHEET 1 AA 2 ILE A 804 MET A 806 0 SHEET 2 AA 2 CYS A1024 HIS A1026 -1 O ILE A1025 N VAL A 805 SHEET 1 AB 5 LEU A 834 ARG A 842 0 SHEET 2 AB 5 GLY A 846 PHE A 854 -1 O VAL A 848 N LEU A 840 SHEET 3 AB 5 CYS A 862 LEU A 870 -1 O ARG A 863 N ALA A 853 SHEET 4 AB 5 MET A 913 GLU A 917 -1 O VAL A 914 N LYS A 868 SHEET 5 AB 5 LEU A 901 CYS A 905 -1 N LEU A 902 O ILE A 915 SHEET 1 AC 2 ILE A1034 LEU A1036 0 SHEET 2 AC 2 VAL A1042 ILE A1044 -1 O LYS A1043 N LEU A1035 SHEET 1 AD 2 VAL A1060 LYS A1062 0 SHEET 2 AD 2 ALA A1065 LEU A1067 -1 O ALA A1065 N LYS A1062 CISPEP 1 LEU A 811 PRO A 812 0 3.03 SITE 1 AC1 18 LEU A 840 VAL A 848 ALA A 866 LYS A 868 SITE 2 AC1 18 GLU A 885 VAL A 899 VAL A 914 VAL A 916 SITE 3 AC1 18 GLU A 917 PHE A 918 CYS A 919 LYS A 920 SITE 4 AC1 18 GLY A 922 LEU A1035 CYS A1045 ASP A1046 SITE 5 AC1 18 PHE A1047 HOH A2029 CRYST1 139.492 56.922 50.787 90.00 97.12 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 0.007169 0.000000 0.000895 0.00000 SCALE2 0.000000 0.017568 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019843 0.00000