MolNFT v1 · #118239 · protein
Human vascular endothelial growth factor receptor 2 (kdr) kinase domain in complex with AAL993
5EW3: “Human vascular endothelial growth factor receptor 2 (kdr) kinase domain in complex with AAL993”. X-ray diffraction, 1 ligand (5T2), 3 pockets (best druggability 0.71). MolNFT v1 #118239 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5EW3
- Type
- protein
- Length
- 540 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
- 5T2
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 274 | 40% helix, 18% strand | P35968 |
| B | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 266 | 40% helix, 18% strand | P35968 |
Ligands and binding sites
- 5T2 · 2-(pyridin-4-ylmethylamino)-~{N}-[3-(trifluoromethyl)phenyl]benzamide · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.71 | 0.84 | 40 | 5T2 |
| 2 | 268 | 0.69 | 0.84 | 38 | 5T2 |
| 3 | 61 | 0.28 | 0.73 | 12 | empty |
Compared structures
- 5EW3 · Human Vascular Endothelial Growth Factor Receptor 2 (KDR) Kinase Domain in complex with… · 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 5EW3 · PDBe 5EW3 · UniProt P35968
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