Research workbench
Crystal structure of VEGFR2 with a benzimidazole-urea inhibitor
Analyse Crystal structure of VEGFR2 with a benzimidazole-urea inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OH4
- Type
- protein
- Length
- 299 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor receptor 2
- EC
- 2.7.10.1
- UniProt
- P35968
- Ligands
- GIG, SO4
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 299 | 40% helix, 16% strand | P35968 |
Ligands and binding sites
- GIG · Methyl (5-{4-[({[2-fluoro-5-(trifluoromethyl)phenyl]amino}carbonyl)amino]phenoxy}-1H-benzimidazol-2-yl)carbamate · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.71 | 0.83 | 43 | GIG |
| 2 | 141 | 0.40 | 0.74 | 26 | SO4 |
| 3 | 109 | 0.39 | 0.75 | 16 | SO4 |
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2OH4 · Crystal structure of Vegfr2 with a benzimidazole-urea inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P35968 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor receptor 2… · a predicted model of the same protein · chain A against A, TM-score 0.93
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P35968
- Elsewhere: RCSB PDB 2OH4 · PDBe 2OH4 · UniProt P35968
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