5oyj

Crystal structure of VEGFR-2 domains 4-5 in complex with DARPin D4b

Method: X-RAY DIFFRACTION D_max: 112.1 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

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 4 其他Polymer 10 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 326–549 Chain D； UniProt 326–549	Not recorded	DARPin D4b × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 7 alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose × 3 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

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 5OYJ	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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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
3EWH Crystal structure of the VEGFR2 kinase domain in complex with a pyridyl-pyrimidine benzimidazole inhibitor Deposited 2008-10-15	Different construct Different mutation/modification Different oligomeric state 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 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
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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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
6GQO Crystal structure of human KDR (VEGFR2) kinase domain in complex with AZD3229-analogue (compound 18) Deposited 2018-06-07	Different construct Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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	2
Chains and sequence ranges	Author chain C； PDBConstruct 5–228； UniProt 326–549 Author chain D； PDBConstruct 5–228； UniProt 326–549

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5oyj
Deposition date deposition_date	2017-09-10
Structure title title	Crystal structure of VEGFR-2 domains 4-5 in complex with DARPin D4b
Keywords keywords	glycoprotein receptor kinase designed ankyrin repeat protein angiogenesis, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	35.60 Å
Radius of gyration Rg (electron density) rg_electron	34.68 Å
Forward intensity I(0) i0	121415000.00
Molecular weight molecular_weight	87971.0 kDa
Excluded volume excluded_volume	110070 Å³
Envelope volume envelope_volume	157660 Å³
Hydration-shell volume shell_volume	38173 Å³
Envelope diameter envelope_diameter	114.5 Å
Shell Rg shell_rg	40.99 Å
Envelope Rg envelope_rg	33.91 Å
Shape Rg shape_rg	34.67 Å
Total Rg total_rg	35.20 Å
Total atoms total_atoms	6194
Residues n_residues	759
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	112.1 Å
Rg (real space) rg_real	35.47 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.2140e+08
I(0) uncertainty (real space) i0_real_error	2.0130e+06
Rg (reciprocal space) rg_reciprocal	35.55 Å
I(0) (reciprocal space) i0_reciprocal	121400000.0000
Solution quality estimate total_estimate	0.8911
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	48.4 Å
Skewness Skewness skewness	0.088
Kurtosis Kurtosis kurtosis	-0.536
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9908000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.874

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	DARPin D4b
Molecular weight formula_weight	18339.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6506

MRGSHHHHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNAHDQNGFTPLHLAAWYGHLEIVGVLLKNGADVNAFDKYGFTPLHLAAEEGHLEVVEVLLKYGADVNAKDEHGSTPLHLAADIGHLEIVEVLLKNGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN

来源 Source

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Vascular endothelial growth factor receptor 2
Molecular weight formula_weight	26253.7 kDa
EC 编号 ec_number	2.7.10.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

APLAEKPFVAFGSGMESLVEATVGERVRIPAKYLGYPPPEIKWYKNGIPLESNHTIKAGHVLTIMEVSERDTGNYTVILTNPISKEKQSHVVSLVVYVPPQIGEKSLISPVDSYQYGTTQTLTCTVYAIPPPHHIHWYWQLEEECANEPSQAVSVTNPYPCEEWRSVEDFQGGNKIEVNKNQFALIEGKNKTVSTLVIQAANVSALYKCEAVNKVGRGERVISFHVTRHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	7

Entity 4 Entity 4 branched

Description description	alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	270

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5oyjA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	5oyjB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	5oyjC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5oyjC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5oyjD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5oyjD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	109.489 Å
Unit-cell length b length_b	164.559 Å
Unit-cell length c length_c	70.759 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.380 Å
Low-resolution limit resolution_low	38.749 Å
R factor r_factor	0.1804
R_work r_work	0.1779
R_free r_free	0.2288

fit	/app/data/saxs_computation/oy/5oyj/5oyj.fit
pddf	/app/data/pr_computation/oy/5oyj/5oyj.pr.out
profile	/app/data/saxs_computation/oy/5oyj/5oyj.dat

Crystal structure of VEGFR-2 domains 4-5 in complex with DARPin D4b

1. Protein Identity and Related Structures Protein Identity & Related Structures

Vascular endothelial growth factor receptor 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)