Research workbench
Crystal structure of the VEGFR2 kinase domain in complex with a pyridone inhibitor
Analyse Crystal structure of the VEGFR2 kinase domain in complex with a pyridone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CPC
- Type
- protein
- Length
- 546 residues
- Chains
- 2
- 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
- C52
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 284 | 46% helix, 15% strand | P35968 |
| B | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 262 | 44% helix, 17% strand | P35968 |
Ligands and binding sites
- C52 · 3-(2-aminoquinazolin-6-yl)-4-methyl-1-[3-(trifluoromethyl)phenyl]pyridin-2(1H)-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.72 | 0.86 | 30 | C52 |
| 2 | 272 | 0.72 | 0.86 | 32 | C52 |
| 3 | 437 | 0.61 | 0.76 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 468 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3CPC · Crystal structure of the VEGFR2 kinase domain in complex with a pyridone 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 B against A, TM-score 0.97
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 3CPC · PDBe 3CPC · UniProt P35968
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