Research workbench
Crystal structure of the VEGFR2 kinase domain in complex with motesanib
Analyse Crystal structure of the VEGFR2 kinase domain in complex with motesanib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EFL
- Type
- protein
- Length
- 549 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
- 706
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 286 | 45% helix, 16% strand | P35968 |
| B | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 263 | 44% helix, 19% strand | P35968 |
Ligands and binding sites
- 706 · N-(3,3-dimethyl-2,3-dihydro-1H-indol-6-yl)-2-[(pyridin-4-ylmethyl)amino]pyridine-3-carboxamide · ligand · 2 copies · chains A, B
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 | 359 | 0.71 | 0.83 | 48 | 706 |
| 2 | 363 | 0.70 | 0.83 | 41 | 706 |
| 3 | 377 | 0.64 | 0.78 | 30 | empty |
| 4 | 54 | 0.32 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 494 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3EFL · Crystal structure of the VEGFR2 kinase domain in complex with motesanib · the same entry in another collection · chain A against A, TM-score 1.00
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 3EFL · PDBe 3EFL · UniProt P35968
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