MolNFT v1 · #83982 · protein
Kdr in complex with ligand lenvatinib
3WZD · Vascular endothelial growth factor receptor 2: “Kdr in complex with ligand lenvatinib”. X-ray diffraction, 2 ligands (LEV, SO4), 2 pockets (best druggability 0.64). MolNFT v1 #83982 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3WZD
- Type
- protein
- Length
- 278 residues
- Chains
- 1
- 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
- LEV, SO4
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor receptor 2 (EC 2.7.10.1) | protein | 278 | 44% helix, 15% strand | P35968 |
Ligands and binding sites
- LEV · 4-{3-chloro-4-[(cyclopropylcarbamoyl)amino]phenoxy}-7-methoxyquinoline-6-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.64 | 0.82 | 26 | LEV, GOL |
| 2 | 75 | 0.42 | 0.80 | 16 | empty |
Modifications
Observed in the structure: 4 covalent (additive adduct).
Compared structures
- 3WZD · KDR in complex with ligand lenvatinib · 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 3WZD · PDBe 3WZD · UniProt P35968
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