MolNFT v1 · #58607 · protein
Crystal structure of the VEGFR2 kinase domain in complex with a naphthamide inhibitor
3B8R · Vascular endothelial growth factor receptor 2: “Crystal structure of the VEGFR2 kinase domain in complex with a naphthamide inhibitor”. X-ray diffraction, 1 ligand (887), 4 pockets (best druggability 0.69). MolNFT v1 #58607 on…
- PDB
- 3B8R
- Type
- protein
- Length
- 556 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
- 887
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 289 | 45% helix, 15% strand | P35968 |
| B | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 267 | 44% helix, 16% strand | P35968 |
Ligands and binding sites
- 887 · N-cyclopropyl-6-[(6,7-dimethoxyquinolin-4-yl)oxy]naphthalene-1-carboxamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.69 | 0.79 | 53 | empty |
| 2 | 192 | 0.65 | 0.84 | 26 | 887 |
| 3 | 186 | 0.64 | 0.84 | 27 | 887 |
| 4 | 53 | 0.28 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 505 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3B8R · 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 0.98
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 3B8R · PDBe 3B8R · UniProt P35968
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