Research workbench
Crystal structure of the VEGFR2 kinase domain in complex with a naphthamide inhibitor
Analyse Crystal structure of the VEGFR2 kinase domain in complex with a naphthamide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B8Q
- Type
- protein
- Length
- 563 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
- 900
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 292 | 46% helix, 17% strand | P35968 |
| B | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 271 | 41% helix, 17% strand | P35968 |
Ligands and binding sites
- 900 · N-(4-chlorophenyl)-6-[(6,7-dimethoxyquinolin-4-yl)oxy]naphthalene-1-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.70 | 0.83 | 32 | 900 |
| 2 | 325 | 0.69 | 0.83 | 32 | 900 |
| 3 | 505 | 0.66 | 0.77 | 35 | empty |
| 4 | 105 | 0.41 | 0.76 | 16 | empty |
| 5 | 74 | 0.33 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 496 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3B8Q · Crystal structure of the VEGFR2 kinase domain in complex with a naphthamide 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 3B8Q · PDBe 3B8Q · UniProt P35968
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