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3ewh

Crystal structure of the VEGFR2 kinase domain in complex with a pyridyl-pyrimidine benzimidazole inhibitor

Method: X-RAY DIFFRACTION Dmax: 72.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

vascular endothelial growth factor receptor 2

Homo sapiens

UniProt P35968

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 815–939 Chain A； UniProt 990–1171 Fragment：UNP residues 815-939, 990-1171 Mutation：C817A, V916T, E990V K11 N-[4-({3-[2-(methylamino)pyrimidin-4-yl]pyridin-2-yl}oxy)naphthalen-1-yl]-6-(trifluoromethyl)-1H-benzimidazol-2-amine × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；277 K；PEG 5000 MME, HEPES, ammonium sulfate, sodium chloride, isopropanol, beta-mercaptoethanol , pH 8.0, VAPOR DIFFUSION, temperature 277K Resolution 1.60 Å R-free 0.234

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3EWH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1VR2 HUMAN VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2 (KDR) KINASE DOMAIN Deposited 1998-12-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–939（134 aa） Fragment：KINASE DOMAIN
Chain A 990–1171（182 aa） Fragment：KINASE DOMAIN
Mutation：E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E990V Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.2
Resolution 2.40 Å
1Y6A Crystal structure of VEGFR2 in complex with a 2-anilino-5-aryl-oxazole inhibitor Deposited 2004-12-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–1171（366 aa）
Not recorded AAZ N-[5-(ETHYLSULFONYL)-2-METHOXYPHENYL]-5-[3-(2-PYRIDINYL)PHENYL]-1,3-OXAZOL-2-AMINE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.217
1Y6B Crystal structure of VEGFR2 in complex with a 2-anilino-5-aryl-oxazole inhibitor Deposited 2004-12-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–1171（366 aa）
Not recorded AAX N-(CYCLOPROPYLMETHYL)-4-(METHYLOXY)-3-({5-[3-(3-PYRIDINYL)PHENYL]-1,3-OXAZOL-2-YL}AMINO)BENZENESULFONAMIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.236
1YWN Vegfr2 in complex with a novel 4-amino-furo[2,3-d]pyrimidine Deposited 2005-02-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–1171（366 aa） Fragment：Kinase Domain
Mutation：E990V, Deletion of residues 940-989 Non-standard monomer：Yes (specific site not provided by mmCIF) LIF N-{4-[4-AMINO-6-(4-METHOXYPHENYL)FURO[2,3-D]PYRIMIDIN-5-YL]PHENYL}-N'-[2-FLUORO-5-(TRIFLUOROMETHYL)PHENYL]UREA × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 1.71 Å R-free 0.230
2M59 Spatial structure of dimeric VEGFR2 membrane domain in DPC micelles Deposited 2013-02-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 759–795（37 aa） Fragment：UNP residues 759-795
Chain B 759–795（37 aa） Fragment：UNP residues 759-795
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；318 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition 0.6 mM VEGFR2tm, 0.6 mM [U-100% 13C; U-100% 15N] VEGFR2tm, 48 mM [U-100% 2H] DPC, 20 mM [U-99% 2H] sodium acetate, 3 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MET NMR spatial structure of the trimeric mutant TM domain of VEGFR2 receptor. Deposited 2013-10-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 759–795（37 aa） Fragment：UNP residues 759-795
Chain B 759–795（37 aa） Fragment：UNP residues 759-795
Chain C 759–795（37 aa） Fragment：UNP residues 759-795
Mutation：V11E Mutation：V11E Mutation：V11E No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；318 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition 0.6mM VEGFR-2tm769-1, 0.6mM [U-100% 13C; U-100% 15N] VEGFR-2tm769-2, 120mM [U-100% 2H] DPC-3, 20mM [U-99% 2H] sodium acetate-4, 3mM sodium azide-5, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MEU NMR spatial structure of mutant dimeric TM domain of VEGFR2 receptor Deposited 2013-10-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 759–795（37 aa） Fragment：UNP residues 759-795
Chain B 759–795（37 aa） Fragment：UNP residues 759-795
Mutation：G12E, F19E Mutation：G12E, F19E No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；318 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition 0.6mM v2e_707-1, 0.6mM [U-100% 13C; U-100% 15N] v2e_707-2, 120mM [U-100% 2H] DPC-3, 20mM [U-99% 2H] sodium acetate-4, 3mM sodium azide-5, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2OH4 Crystal structure of Vegfr2 with a benzimidazole-urea inhibitor Deposited 2007-01-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–940（135 aa） Fragment：kinase domain
Chain A 992–1171（180 aa） Fragment：kinase domain
Mutation：E990V, Deletion of residues 940-989 Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E990V, Deletion of residues 940-989 Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 GIG METHYL (5-{4-[({[2-FLUORO-5-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-1H-BENZIMIDAZOL-2-YL)CARBAMATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.05 Å R-free 0.231
2P2H Crystal structure of the VEGFR2 kinase domain in complex with a pyridinyl-triazine inhibitor Deposited 2007-03-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 815–939（125 aa） Fragment：kinase domain
Chain A 990–1171（182 aa） Fragment：kinase domain
Mutation：C817A, V916T, E990V, (delete 940-989) Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V, (delete 940-989) Non-standard monomer：Yes (specific site not provided by mmCIF) 994 4-(2-anilinopyridin-3-yl)-N-(3,4,5-trimethoxyphenyl)-1,3,5-triazin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.229
2P2I Crystal structure of the VEGFR2 kinase domain in complex with a nicotinamide inhibitor Deposited 2007-03-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 815–939（125 aa） Fragment：kinase domain
Chain A 990–1171（182 aa） Fragment：kinase domain
Mutation：C817A, E990V, (delete 940-989) Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, E990V, (delete 940-989) Non-standard monomer：Yes (specific site not provided by mmCIF) 608 N-(4-phenoxyphenyl)-2-[(pyridin-4-ylmethyl)amino]nicotinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.40 Å R-free 0.266
2P2I Crystal structure of the VEGFR2 kinase domain in complex with a nicotinamide inhibitor Deposited 2007-03-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 815–939（125 aa） Fragment：kinase domain
Chain B 990–1171（182 aa） Fragment：kinase domain
Mutation：C817A, E990V, (delete 940-989) Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, E990V, (delete 940-989) Non-standard monomer：Yes (specific site not provided by mmCIF) 608 N-(4-phenoxyphenyl)-2-[(pyridin-4-ylmethyl)amino]nicotinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.40 Å R-free 0.266
2QU5 Crystal structure of the VEGFR2 kinase domain in complex with a benzimidazole inhibitor Deposited 2007-08-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 815–939（125 aa） Fragment：kinase domain
Chain A 990–1171（182 aa） Fragment：kinase domain
Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) 276 4-[[2-[[4-chloro-3-(trifluoromethyl)phenyl]amino]-3H-benzimidazol-5-yl]oxy]-N-methyl-pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；277 K；PEG 4000, lithum sulfate, Tris, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.95 Å R-free 0.251
2QU6 Crystal structure of the VEGFR2 kinase domain in complex with a benzoxazole inhibitor Deposited 2007-08-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 815–939（125 aa） Fragment：kinase domain
Chain A 990–1171（182 aa） Fragment：kinase domain
Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 857 4-({2-[(4-chloro-3-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}phenyl)amino]-1,3-benzoxazol-5-yl}oxy)-N-methylpyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；PEG 5000 MME, ammonium sulfate, sodium chloride, HEPES, isopropanol, beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.272
2QU6 Crystal structure of the VEGFR2 kinase domain in complex with a benzoxazole inhibitor Deposited 2007-08-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 815–939（125 aa） Fragment：kinase domain
Chain B 990–1171（182 aa） Fragment：kinase domain
Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) 857 4-({2-[(4-chloro-3-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}phenyl)amino]-1,3-benzoxazol-5-yl}oxy)-N-methylpyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；PEG 5000 MME, ammonium sulfate, sodium chloride, HEPES, isopropanol, beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.272
2RL5 Crystal structure of the VEGFR2 kinase domain in complex with a 2,3-dihydro-1,4-benzoxazine inhibitor Deposited 2007-10-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 815–939（125 aa） Fragment：protein kinase domain, residues 940-989 deleted
Chain A 990–1171（182 aa） Fragment：protein kinase domain, residues 940-989 deleted
Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) 2RL N-(4-CHLOROPHENYL)-7-[(6,7-DIMETHOXYQUINOLIN-4-YL)OXY]-2,3-DIHYDRO-1,4-BENZOXAZINE-4-CARBOXAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；277 K；PEG 4000, lithium sulfate, Tris, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.65 Å R-free 0.233
2X1W Crystal Structure of VEGF-C in Complex with Domains 2 and 3 of VEGFR2 Deposited 2010-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain M 120–326（207 aa） Fragment：IG-LIKE DOMAINS 2 AND 3, RESIDUES 120-326
Chain N 120–326（207 aa） Fragment：IG-LIKE DOMAINS 2 AND 3, RESIDUES 120-326
Not recorded CS CESIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.2；100 MM MES BUFFER, PH 5.0-5.6, 50 MM CSCL AND 28-32 % (W/V) JEFFAMINE 600.
Resolution 2.70 Å R-free 0.280
2X1W Crystal Structure of VEGF-C in Complex with Domains 2 and 3 of VEGFR2 Deposited 2010-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 120–326（207 aa） Fragment：IG-LIKE DOMAINS 2 AND 3, RESIDUES 120-326
Chain O 120–326（207 aa） Fragment：IG-LIKE DOMAINS 2 AND 3, RESIDUES 120-326
Not recorded CS CESIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.2；100 MM MES BUFFER, PH 5.0-5.6, 50 MM CSCL AND 28-32 % (W/V) JEFFAMINE 600.
Resolution 2.70 Å R-free 0.280
2X1X CRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH DOMAINS 2 AND 3 OF VEGFR2 IN A TETRAGONAL CRYSTAL FORM Deposited 2010-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 120–326（207 aa） Fragment：IG-LIKE DOMAINS 2 AND 3, RESIDUES 120-326
Not recorded HG MERCURY (II) ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；100 MM NA-ACETATE BUFFER, PH 4.4-4.8, 50 MM CSCL, 28-32 % (W/V) JEFFAMINE 600
Resolution 3.10 Å R-free 0.334
2XIR Crystal structure of the VEGFR2 kinase domain in complex with PF- 00337210 (N,2-dimethyl-6-(7-(2-morpholinoethoxy)quinolin-4-yloxy) benzofuran-3-carboxamide) Deposited 2010-06-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–939（134 aa） Fragment：KINASE DOMAIN, RESIDUES 806-939,990-1171
Chain A 990–1171（182 aa） Fragment：KINASE DOMAIN, RESIDUES 806-939,990-1171
Mutation：YES Mutation：YES 00J N,2-DIMETHYL-6-{[7-(2-MORPHOLIN-4-YLETHOXY)QUINOLIN-4-YL]OXY}-1-BENZOFURAN-3-CARBOXAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；286 K；PROTEIN PRODUCTION, PROTEIN PURIFICATION, AND COCRYSTALLIZATION WERE PERFORMED AS PREVIOUSLY DESCRIBED (PUBLISHED INTERNATIONAL PATENT APPLICATION WO 2004/092217 HANGING DROP VAPOR DIFFUSION AT 13 DEGREES C. 2 MICROLITERS OF A 7.7 MG/ML PROTEIN SOLUTION (IN 50 MM HEPES 7.5, 30 MM SODIUM CHLORIDE, 5 MM DTT, AND 5% DMSO) WAS MIXED WITH 2 MICROLITERS OF CRYSTALLIZATION SOLUTION (100 MM HEPES PH 7.5, 20% PEG 6K AND 5% MPD) AND SUSPENDED OVER 1 ML OF CRYSTALLIZATION SOLUTION PLUS 5 MICROLITERS BME.
Resolution 1.50 Å R-free 0.238
3B8Q Crystal structure of the VEGFR2 kinase domain in complex with a naphthamide inhibitor Deposited 2007-11-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 815–939（125 aa） Fragment：kinase domain; UNP residues 815-939, 990-1171
Chain A 990–1171（182 aa） Fragment：kinase domain; UNP residues 815-939, 990-1171
Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) 900 N-(4-chlorophenyl)-6-[(6,7-dimethoxyquinolin-4-yl)oxy]naphthalene-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；PEG 5000 MME, HEPES, sodium chloride, ammonium sulfate, isopropanol, beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 2.75 Å R-free 0.276
3B8Q Crystal structure of the VEGFR2 kinase domain in complex with a naphthamide inhibitor Deposited 2007-11-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 815–939（125 aa） Fragment：kinase domain; UNP residues 815-939, 990-1171
Chain B 990–1171（182 aa） Fragment：kinase domain; UNP residues 815-939, 990-1171
Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) 900 N-(4-chlorophenyl)-6-[(6,7-dimethoxyquinolin-4-yl)oxy]naphthalene-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；PEG 5000 MME, HEPES, sodium chloride, ammonium sulfate, isopropanol, beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 2.75 Å R-free 0.276
3B8R Crystal structure of the VEGFR2 kinase domain in complex with a naphthamide inhibitor Deposited 2007-11-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 815–939（125 aa） Fragment：kinase domain; UNP residues 815-939, 990-1171
Chain A 990–1171（182 aa） Fragment：kinase domain; UNP residues 815-939, 990-1171
Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 887 N-cyclopropyl-6-[(6,7-dimethoxyquinolin-4-yl)oxy]naphthalene-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；PEG 5000 MME, HEPES, sodium chloride, ammonium sulfate, isopropanol, beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 2.70 Å R-free 0.259
3B8R Crystal structure of the VEGFR2 kinase domain in complex with a naphthamide inhibitor Deposited 2007-11-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 815–939（125 aa） Fragment：kinase domain; UNP residues 815-939, 990-1171
Chain B 990–1171（182 aa） Fragment：kinase domain; UNP residues 815-939, 990-1171
Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) 887 N-cyclopropyl-6-[(6,7-dimethoxyquinolin-4-yl)oxy]naphthalene-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；PEG 5000 MME, HEPES, sodium chloride, ammonium sulfate, isopropanol, beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 2.70 Å R-free 0.259
3BE2 Crystal structure of the VEGFR2 kinase domain in complex with a benzamide inhibitor Deposited 2007-11-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 815–939（125 aa） Fragment：kinase domain, residues 815-939 and 990-1171
Chain A 990–1171（182 aa） Fragment：kinase domain, residues 815-939 and 990-1171
Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) RAJ N-{3-[3-(DIMETHYLAMINO)PROPYL]-5-(TRIFLUOROMETHYL)PHENYL}-4-METHYL-3-[(3-PYRIMIDIN-4-YLPYRIDIN-2-YL)AMINO]BENZAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；PEG 5000 MME, HEPES, sodium chloride, ammonium sulfate, isopropanol, beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 1.75 Å R-free 0.226
3C7Q Structure of VEGFR2 kinase domain in complex with BIBF1120 Deposited 2008-02-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–1171（366 aa） Fragment：kinase domain
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 5 XIN methyl (3Z)-3-{[(4-{methyl[(4-methylpiperazin-1-yl)acetyl]amino}phenyl)amino](phenyl)methylidene}-2-oxo-2,3-dihydro-1H-indole-6-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；0.1M HEPES, 2.1M Ammonium Sulphate, 3% PEG MME 550, 10mM Beta-Mercaptoethanol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.279
3CJF Crystal structure of VEGFR2 in complex with a 3,4,5-trimethoxy aniline containing pyrimidine Deposited 2008-03-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–939（134 aa） Fragment：kinase domain; residues 806-939 and 994-1168
Chain A 994–1168（175 aa） Fragment：kinase domain; residues 806-939 and 994-1168
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 4 SAV N~4~-(3-methyl-1H-indazol-6-yl)-N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.15 Å R-free 0.258
3CJG Crystal structure of VEGFR2 in complex with a 3,4,5-trimethoxy aniline containing pyrimidine Deposited 2008-03-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–939（134 aa） Fragment：Kinase domain; residues 806-939 and 994-1168
Chain A 994–1168（175 aa） Fragment：Kinase domain; residues 806-939 and 994-1168
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 KIM N~4~-methyl-N~4~-(3-methyl-1H-indazol-6-yl)-N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.25 Å R-free 0.253
3CP9 Crystal structure of the VEGFR2 kinase domain in complex with a pyridone inhibitor Deposited 2008-03-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 815–939（125 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 940-989 DELETED
Chain A 990–1171（182 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 940-989 DELETED
Mutation：C817A, V916T, E990V, delete(940-989) Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V, delete(940-989) Non-standard monomer：Yes (specific site not provided by mmCIF) C19 3-(2-aminoquinazolin-6-yl)-1-(3,3-dimethylindolin-6-yl)-4-methylpyridin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；PEG 5000 MME, HEPES, ammonium sulfate, sodium chloride, isopropanol, beta-mercaptoethanol , pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 2.50 Å R-free 0.263
3CP9 Crystal structure of the VEGFR2 kinase domain in complex with a pyridone inhibitor Deposited 2008-03-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 815–939（125 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 940-989 DELETED
Chain B 990–1171（182 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 940-989 DELETED
Mutation：C817A, V916T, E990V, delete(940-989) Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V, delete(940-989) Non-standard monomer：Yes (specific site not provided by mmCIF) C19 3-(2-aminoquinazolin-6-yl)-1-(3,3-dimethylindolin-6-yl)-4-methylpyridin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；PEG 5000 MME, HEPES, ammonium sulfate, sodium chloride, isopropanol, beta-mercaptoethanol , pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 2.50 Å R-free 0.263
3CPB Crystal structure of the VEGFR2 kinase domain in complex with a bisamide inhibitor Deposited 2008-03-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 815–939（125 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 940-989 DELETED
Chain A 990–1171（182 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 940-989 DELETED
Mutation：E817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) C92 N'-(6-aminopyridin-3-yl)-N-(2-cyclopentylethyl)-4-methyl-benzene-1,3-dicarboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；PEG 5000 MME, HEPES, ammonium sulfate, sodium chloride, isopropanol, beta-mercaptoethanol , pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 2.70 Å R-free 0.286
3CPB Crystal structure of the VEGFR2 kinase domain in complex with a bisamide inhibitor Deposited 2008-03-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 815–939（125 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 940-989 DELETED
Chain B 990–1171（182 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 940-989 DELETED
Mutation：E817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) C92 N'-(6-aminopyridin-3-yl)-N-(2-cyclopentylethyl)-4-methyl-benzene-1,3-dicarboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；PEG 5000 MME, HEPES, ammonium sulfate, sodium chloride, isopropanol, beta-mercaptoethanol , pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 2.70 Å R-free 0.286
3CPC Crystal structure of the VEGFR2 kinase domain in complex with a pyridone inhibitor Deposited 2008-03-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 815–939（125 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 940-989 DELETED
Chain A 990–1171（182 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 940-989 DELETED
Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) C52 3-(2-aminoquinazolin-6-yl)-4-methyl-1-[3-(trifluoromethyl)phenyl]pyridin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；PEG 5000 MME, HEPES, ammonium sulfate, sodium chloride, isopropanol, beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 2.40 Å R-free 0.272
3CPC Crystal structure of the VEGFR2 kinase domain in complex with a pyridone inhibitor Deposited 2008-03-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 815–939（125 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 940-989 DELETED
Chain B 990–1171（182 aa） Fragment：PROTEIN KINASE DOMAIN, RESIDUES 940-989 DELETED
Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) C52 3-(2-aminoquinazolin-6-yl)-4-methyl-1-[3-(trifluoromethyl)phenyl]pyridin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；PEG 5000 MME, HEPES, ammonium sulfate, sodium chloride, isopropanol, beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 2.40 Å R-free 0.272
3DTW Crystal structure of the VEGFR2 kinase domain in complex with a benzisoxazole inhibitor Deposited 2008-07-16 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 815–939（125 aa） Fragment：UNP residues 815-939, 990-1171
Chain A 990–1171（182 aa） Fragment：UNP residues 815-939, 990-1171
Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) A96 6-chloro-N-pyrimidin-5-yl-3-{[3-(trifluoromethyl)phenyl]amino}-1,2-benzisoxazole-7-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；polyethylene glycol 5000 monomethyl ether, sodium chloride, ammonium sulfate, isopropanol, HEPES, beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 2.90 Å R-free 0.279
3DTW Crystal structure of the VEGFR2 kinase domain in complex with a benzisoxazole inhibitor Deposited 2008-07-16 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 815–939（125 aa） Fragment：UNP residues 815-939, 990-1171
Chain B 990–1171（182 aa） Fragment：UNP residues 815-939, 990-1171
Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, V916T, E990V Non-standard monomer：Yes (specific site not provided by mmCIF) A96 6-chloro-N-pyrimidin-5-yl-3-{[3-(trifluoromethyl)phenyl]amino}-1,2-benzisoxazole-7-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；polyethylene glycol 5000 monomethyl ether, sodium chloride, ammonium sulfate, isopropanol, HEPES, beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 2.90 Å R-free 0.279
3EFL Crystal structure of the VEGFR2 kinase domain in complex with motesanib Deposited 2008-09-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 815–939（125 aa） Fragment：kinase domain, Unp residues 815-939, 990- 1171
Chain A 990–1171（182 aa） Fragment：kinase domain, Unp residues 815-939, 990- 1171
Mutation：C817A, E990V, 940-989 deletion Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, E990V, 940-989 deletion Non-standard monomer：Yes (specific site not provided by mmCIF) 706 N-(3,3-dimethyl-2,3-dihydro-1H-indol-6-yl)-2-[(pyridin-4-ylmethyl)amino]pyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；PEG 5000 MME, HEPES, ammonium sulfate, sodium chloride, isopropanol, beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 2.20 Å R-free 0.264
3EFL Crystal structure of the VEGFR2 kinase domain in complex with motesanib Deposited 2008-09-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 815–939（125 aa） Fragment：kinase domain, Unp residues 815-939, 990- 1171
Chain B 990–1171（182 aa） Fragment：kinase domain, Unp residues 815-939, 990- 1171
Mutation：C817A, E990V, 940-989 deletion Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C817A, E990V, 940-989 deletion Non-standard monomer：Yes (specific site not provided by mmCIF) 706 N-(3,3-dimethyl-2,3-dihydro-1H-indol-6-yl)-2-[(pyridin-4-ylmethyl)amino]pyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；PEG 5000 MME, HEPES, ammonium sulfate, sodium chloride, isopropanol, beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 2.20 Å R-free 0.264
3KVQ Crystal structure of VEGFR2 extracellular domain D7 Deposited 2009-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 657–764（108 aa） Fragment：Extracellular Domain 7
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；Succinic Acid 0.2M, pH7 PEG3350 18%, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Resolution 2.70 Å R-free 0.296
3S35 Structural basis for the function of two anti-VEGF receptor antibodies Deposited 2011-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain X 220–338（119 aa） Fragment：domain 3 of VEGF receptor 2, UNP residues 220-338
Not recorded CA CALCIUM ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；100 mM CdCl2, 100 mM Na acetate, pH 4.6, 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.20 Å R-free 0.259
3S36 Structural basis for the function of two anti-VEGF receptor antibodies Deposited 2011-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain X 220–338（119 aa） Fragment：domain 3 of VEGF receptor 2, UNP residues 220-338
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M imidazole, pH 6.5; 0.1 M CaCl2, 40% PEG 1500, 10% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.20 Å R-free 0.332
3S37 Structural basis for the function of two anti-VEGF receptor antibodies Deposited 2011-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain X 220–338（119 aa） Fragment：domain 3 of VEGF receptor 2, UNP residues 220-338
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M imidazole, pH 6.5, 0.1 M CaCl2, 40% PEG 1500, 10% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.70 Å R-free 0.315
3U6J Crystal structure of the VEGFR2 kinase domain in complex with a pyrazolone inhibitor Deposited 2011-10-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 815–1171（357 aa） Fragment：unp residues 815-1171
Mutation：V916T, E990V 03X N-{4-[(6,7-dimethoxyquinolin-4-yl)oxy]-3-fluorophenyl}-1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；17% PEG 5000 monomethyl ether, 75 mM ammonium sulfate, 25 mM sodium chloride, 100 mM HEPES, 8% isopropanol, 40 mM beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.15 Å R-free 0.230
3V2A VEGFR-2/VEGF-A COMPLEX STRUCTURE Deposited 2011-12-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–764（764 aa） Fragment：UNP residues 1-764
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M NaCl, 1.6 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.20 Å R-free 0.300
3V6B VEGFR-2/VEGF-E complex structure Deposited 2011-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 132–548（417 aa） Fragment：VEGFR-2, UNP residues 132-548
Mutation：Ig-domains 2-3 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M HEPES (pH 6.5), 0.8 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.21 Å R-free 0.276
3VHE Crystal structure of human VEGFR2 kinase domain with a novel pyrrolopyrimidine inhibitor. Deposited 2011-08-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 811–1169（359 aa） Fragment：KINASE DOMAIN (UNP RESIDUES 811-1169)
Not recorded 42Q 1-{2-fluoro-4-[(5-methyl-5H-pyrrolo[3,2-d]pyrimidin-4-yl)oxy]phenyl}-3-[3-(trifluoromethyl)phenyl]urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；1.3M tri-sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.55 Å R-free 0.209
3VHK Crystal structure of the VEGFR2 kinase domain in complex with a back pocket binder Deposited 2011-08-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–1171（366 aa） Fragment：UNP RESIDUES 806-1171
Not recorded BPK {3-[(5-methyl-2-phenyl-1,3-oxazol-4-yl)methoxy]phenyl}methanol × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；100mM HEPES, 880-1440mM tri-sodium citrate, pH 7.0-8.0, vapor diffusion, sitting drop, temperature 293K
Resolution 2.49 Å R-free 0.262
3VID Crystal structure of human VEGFR2 kinase domain with Compound A. Deposited 2011-09-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 813–1168（356 aa） Fragment：KINASE DOMAIN (UNP RESIDUES 813-1168)
Not recorded 4TT 4,5,6,11-tetrahydro-1H-pyrazolo[4',3':6,7]cyclohepta[1,2-b]indole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；1.3M TRI-SODIUM CITRATE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.30 Å R-free 0.281
3VNT Crystal Structure of the Kinase domain of Human VEGFR2 with a [1,3]thiazolo[5,4-b]pyridine derivative Deposited 2012-01-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–1171（366 aa） Fragment：UNP residues 806-1171
Mutation：truncated residues 940-989 0JA 2-chloro-3-(1-cyanocyclopropyl)-N-[5-({2-[(cyclopropylcarbonyl)amino][1,3]thiazolo[5,4-b]pyridin-5-yl}oxy)-2-fluorophenyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100mM HEPES, 880-1440mM tri-sodium citrate, pH 7.0-8.0, vapor diffusion, sitting drop, temperature 293K
Resolution 1.64 Å R-free 0.192
3VO3 Crystal Structure of the Kinase domain of Human VEGFR2 with imidazo[1,2-b]pyridazine derivative Deposited 2012-01-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–1171（366 aa） Fragment：UNP residues 806-1171
Mutation：truncated residues 940-989 0KF N-[3-({2-[(cyclopropylcarbonyl)amino]imidazo[1,2-b]pyridazin-6-yl}oxy)phenyl]-1,3-dimethyl-1H-pyrazole-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M trisHCl pH 8.5, 1.2M tri-sodium citrate, vapor diffusion, sitting drop, temperature 293K
Resolution 1.52 Å R-free 0.182
3WZD KDR in complex with ligand lenvatinib Deposited 2014-09-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 814–1172（359 aa） Fragment：kinase domain (UNP RESIDUES 814-940, 991-1172)
Mutation：T940V LEV 4-{3-chloro-4-[(cyclopropylcarbamoyl)amino]phenoxy}-7-methoxyquinoline-6-carboxamide × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 4 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 9.5；277 K；0.1M CHES,5-20% PEG 8000, pH 9.5, VAPOR DIFFUSION, temperature 277K
Resolution 1.57 Å R-free 0.212
3WZE KDR in complex with ligand sorafenib Deposited 2014-09-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 814–1172（359 aa） Fragment：kinase domain (UNP RESIDUES 814-940, 991-1172)
Mutation：T940V BAX 4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-N-METHYLPYRIDINE-2-CARBOXAMIDE × 1 ACT ACETATE ION × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；10-25% PEG 3350, Na3Citrate, 0.1M Bis-Tris propane, pH 8.0, VAPOR DIFFUSION, temperature 277K
Resolution 1.90 Å R-free 0.224
4AG8 CRYSTAL STRUCTURE OF THE VEGFR2 KINASE DOMAIN IN COMPLEX WITH AXITINIB (AG-013736) (N-Methyl-2-(3-((E)-2-pyridin-2-yl-vinyl)-1H- indazol-6-ylsulfanyl)-benzamide) Deposited 2012-01-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–939（134 aa） Fragment：KINASE DOMAIN, RESIDUES 806-940,990-1171
Chain A 990–1171（182 aa） Fragment：KINASE DOMAIN, RESIDUES 806-940,990-1171
Mutation：YES Mutation：YES AXI AXITINIB × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；CRYSTALS WERE GROWN AT 4 OR 13 C BY THE HANGING DROP VAPOR DIFFUSION BY MIXING 2 MICORLITERS OF PROTEIN-INHIBITOR COMPLEX SOLUTION WITH 2 MICROLITERS OF MOTHER LIQUOR (100 MM HEPES (PH 7.5), 200 MM AMMONIUM SULFATE, 5% (V/V) MPD, AND 15-20% (W/V) POLYETHYLENE GLYCOL (MW = 6000)). BEFORE SEALING THE COVERSLIPS ABOVE THE RESERVOIRS, BETA-MERCAPTOETHANOL WAS ADDED TO THE RESERVOIRS TO A FINAL CONCENTRATION OF 60 MM. THIS PROCEDURE PRODUCED MICROCRYSTALS THAT WERE SUBSEQUENTLY USED TO SEED MORE CRYSTALLIZATION DROPS AFTER 12-18 HOURS OF EQUILIBRATION.
Resolution 1.95 Å R-free 0.241
4AGC CRYSTAL STRUCTURE OF VEGFR2 (JUXTAMEMBRANE AND KINASE DOMAINS) IN COMPLEX WITH AXITINIB (AG-013736) (N-Methyl-2-(3-((E)-2-pyridin-2-yl- vinyl)-1H-indazol-6-ylsulfanyl)-benzamide) Deposited 2012-01-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 787–939（153 aa） Fragment：JUXTAMEMBRANE AND KINASE DOMAINS, RESIDUES 787-939,990-1171
Chain A 990–1171（182 aa） Fragment：JUXTAMEMBRANE AND KINASE DOMAINS, RESIDUES 787-939,990-1171
Mutation：YES Mutation：YES AXI AXITINIB × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；286 K；CRYSTALS WERE GROWN AT 13 DEGREES C BY THE HANGING DROP VAPOR DIFFUSION METHOD USING PRECIPITANT SOLUTIONS CONTAINING: 0.2M SODIUM CITRATE (PH 6.0 -6.5) AND 14-21% (W/V) POLYETHYLENE GLYCOL MW = 3350
Resolution 2.00 Å R-free 0.251
4AGD CRYSTAL STRUCTURE OF VEGFR2 (JUXTAMEMBRANE AND KINASE DOMAINS) IN COMPLEX WITH SUNITINIB (SU11248) (N-2-diethylaminoethyl)-5-((Z)-(5- fluoro-2-oxo-1H-indol-3-ylidene)methyl)-2,4-dimethyl-1H-pyrrole-3- carboxamide) Deposited 2012-01-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 787–939（153 aa） Fragment：JUXTAMEMBRANE AND KINASE DOMAINS, RESIDUES 787-939,990-1171
Chain A 990–1171（182 aa） Fragment：JUXTAMEMBRANE AND KINASE DOMAINS, RESIDUES 787-939,990-1171
Mutation：YES Mutation：YES B49 N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carbo xamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；286 K；CRYSTALS WERE GROWN AT 13 DEGREES C BY THE HANGING DROP VAPOR DIFFUSION METHOD USING PRECIPITANT SOLUTIONS CONTAINING: 0.222 M SODIUM CITRATE (PH 6.3) AND 17% (W/V) POLYETHYLENE GLYCOL 3350
Resolution 2.81 Å R-free 0.307
4ASD Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with SORAFENIB (BAY 43-9006) Deposited 2012-04-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 787–939（153 aa） Fragment：JUXTAMEMBRANE AND KINASE DOMAINS, RESIDUES 787-939 AND RESIDUES 990-1171
Chain A 990–1171（182 aa） Fragment：JUXTAMEMBRANE AND KINASE DOMAINS, RESIDUES 787-939 AND RESIDUES 990-1171
Mutation：YES Mutation：YES BAX 4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-N-METHYLPYRIDINE-2-CARBOXAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；286 K；CRYSTALS WERE OBTAINED BY THE HANGING DROP VAPOR DIFFUSION METHOD AT 13 DEGREES C USING PRECIPITANT SOLUTIONS CONTAINING APPROXIMATELY: 0.2M SODIUM CITRATE AND 14-21% (W/V) POLYETHYLENE GLYCOL 3350., pH 6.2
Resolution 2.03 Å R-free 0.230
4ASE CRYSTAL STRUCTURE OF VEGFR2 (JUXTAMEMBRANE AND KINASE DOMAINS) IN COMPLEX WITH TIVOZANIB (AV-951) Deposited 2012-04-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 787–1171（385 aa） Fragment：JUXTAMEMBRANE AND KINASE DOMAINS, RESIDUES 787-1171
Mutation：YES AV9 TIVOZANIB × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；286 K；CRYSTALS WERE OBTAINED BY THE HANGING DROP VAPOR DIFFUSION METHOD AT 13 DEGREES C BY THE USING PRECIPITANT SOLUTIONS CONTAINING APPROXIMATELY: 0.2M SODIUM CITRATE AND 14-21% (W/V) POLYETHYLENE GLYCOL 3350., pH 6.2
Resolution 1.83 Å R-free 0.231
5EW3 Human Vascular Endothelial Growth Factor Receptor 2 (KDR) Kinase Domain in complex with AAL993 Deposited 2015-11-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–1171（366 aa） Fragment：kinase domain, residues 806-1171
Mutation：E990V 5T2 2-(pyridin-4-ylmethylamino)-~{N}-[3-(trifluoromethyl)phenyl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；0.1M MES pH6.5, 8% w/v PEG 8000, 0.02M LITHIUM ACETATE
Resolution 2.50 Å R-free 0.254
5EW3 Human Vascular Endothelial Growth Factor Receptor 2 (KDR) Kinase Domain in complex with AAL993 Deposited 2015-11-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 806–1171（366 aa） Fragment：kinase domain, residues 806-1171
Mutation：E990V 5T2 2-(pyridin-4-ylmethylamino)-~{N}-[3-(trifluoromethyl)phenyl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；0.1M MES pH6.5, 8% w/v PEG 8000, 0.02M LITHIUM ACETATE
Resolution 2.50 Å R-free 0.254
5OYJ Crystal structure of VEGFR-2 domains 4-5 in complex with DARPin D4b Deposited 2017-09-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 326–549（224 aa）
Chain D 326–549（224 aa）
Not recorded CA CALCIUM ION × 4 NA SODIUM ION × 1 CAC CACODYLATE ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293.15 K；0.2 M calcium acetate monohydrate, 15% PEG 4000, 0.1 M sodium cacodylate pH 6.4, cryoprotected with 15% trehalose
Resolution 2.38 Å R-free 0.229
6GQO Crystal structure of human KDR (VEGFR2) kinase domain in complex with AZD3229-analogue (compound 18) Deposited 2018-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–939（134 aa）
Chain A 991–1171（181 aa）
Not recorded F82 2-[4-(6,7-dimethoxyquinazolin-4-yl)oxy-2-methoxy-phenyl]-~{N}-(1-propan-2-ylpyrazol-4-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；8 % PEG 8000, 0.1 M Tris pH 8.5
Resolution 1.87 Å R-free 0.207
6GQP Crystal structure of human KDR (VEGFR2) kinase domain in complex with AZD3229-analogue (compound 23) Deposited 2018-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–1171（366 aa）
Not recorded F88 ~{N}-[4-(6,7-dimethoxyquinazolin-4-yl)oxyphenyl]-2-(1-ethylpyrazol-4-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；7 % PEG 8000, 0.1 M PCTP (sodium propionate, sodium cacodylate trihydrate, bis-tris propane) pH 7.8
Resolution 2.09 Å R-free 0.234
6GQQ Crystal structure of human KDR (VEGFR2) kinase domain in complex with AZD3229-analogue (compound 35) Deposited 2018-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–939（134 aa）
Chain A 991–1171（181 aa）
Not recorded F8B ~{N}-[4-(6,7-dimethoxyquinazolin-4-yl)oxyphenyl]-2-(4-propan-2-yl-1,2,3-triazol-1-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；5 % PEG 8000, 0.1 M PCTP (sodium propionate, sodium cacodylate trihydrate, bis-tris propane) pH 7.2
Resolution 1.52 Å R-free 0.204
6XVJ Crystal structure of the KDR (VEGFR2) kinase domain in complex with a type-II inhibitor Deposited 2020-01-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–1171（366 aa） Fragment：protein kinase domain (807-1171 del[940-989])
Mutation：E990V O35 ~{N}-[3-[(dimethylamino)methyl]-5-methyl-phenyl]-2-[3-methoxy-5-(7-methoxyquinolin-4-yl)oxy-pyridin-2-yl]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；25 % PEG550MME, 0.1 M NaCl, 0.1 M TRIS buffer pH 8.5
Resolution 1.78 Å R-free 0.215
6XVK Crystal structure of the KDR (VEGFR2) kinase domain in complex with a type-II inhibitor bearing an acrylamide Deposited 2020-01-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 806–1171（366 aa） Fragment：protein kinase domain (807-1171 del[940-989])
Mutation：E990V O3E ~{N}-(4,4-dimethyl-2-prop-1-ynyl-3,1-benzoxazin-6-yl)-2-[3-methoxy-5-(7-methoxyquinolin-4-yl)oxy-pyridin-2-yl]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；11 % PEG8000, 0.1 M PCTP buffer pH 6.5
Resolution 1.99 Å R-free 0.244

53 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VGFR2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–125； UniProt 815–939 Author chain A； PDBConstruct 126–307； UniProt 990–1171

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3ewh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3ewh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3ewh
Deposition date deposition_date2008-10-15
Structure title titleCrystal structure of the VEGFR2 kinase domain in complex with a pyridyl-pyrimidine benzimidazole inhibitor
Keywords keywordsangiogenesis, receptor tyrosine kinase, DFG-out, Transferase; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.81 Å
Radius of gyration Rg (electron density) rg_electron20.60 Å
Forward intensity I(0) i020989200.00
Molecular weight molecular_weight35017.0 kDa
Excluded volume excluded_volume43938 ų
Envelope volume envelope_volume53009 ų
Hydration-shell volume shell_volume21594 ų
Envelope diameter envelope_diameter73.7 Å
Shell Rg shell_rg26.97 Å
Envelope Rg envelope_rg21.05 Å
Shape Rg shape_rg20.61 Å
Total Rg total_rg21.46 Å
Total atoms total_atoms2467
Residues n_residues300
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax72.4 Å
Rg (real space) rg_real21.75 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real2.0990e+07
I(0) uncertainty (real space) i0_real_error2.5890e+05
Rg (reciprocal space) rg_reciprocal21.76 Å
I(0) (reciprocal space) i0_reciprocal20990000.0000
Solution quality estimate total_estimate0.8100
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.9 Å
Skewness Skewness skewness0.271
Kurtosis Kurtosis kurtosis-0.435
Angular range angular_range— – 0.3650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6666000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3ewha1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd3ewha2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id3ewhA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id3ewhA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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8. Citations (1)

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9. Files and Curves (10)