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 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 806–939 Chain A； UniProt 990–1171 | Fragment：KINASE DOMAIN, RESIDUES 806-940,990-1171 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 |
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 4AG8 | 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 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 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：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 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 |
| 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 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 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 |
| 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 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 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 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 1–134； UniProt 806–939 Author chain A； PDBConstruct 135–316； UniProt 990–1171 |
