MolNFT v1 · #137078 · protein
Crystal structure of human WEE1 kinase domain in complex with pf- 03814735
5VD2 · WEE1-like protein kinase: “Crystal structure of human WEE1 kinase domain in complex with pf- 03814735”. X-ray diffraction, 3 ligands (34W, CL, PO4), 3 pockets (best druggability 0.67). MolNFT v1 #137078 on GenesisL1: 3D structure…
- PDB
- 5VD2
- Type
- protein
- Length
- 258 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- WEE1-like protein kinase
- EC
- 2.7.10.2
- UniProt
- P30291
- Ligands
- 34W, CL, PO4
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | WEE1-like protein kinase (EC 2.7.10.2) | protein | 258 | 40% helix, 21% strand | P30291 |
Ligands and binding sites
- 34W · N-{2-[(1S,4R)-6-{[4-(cyclobutylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-1,2,3,4-tetrahydro-1,4-epiminonaphthalen-9-yl]-2-oxoethyl}acetamide · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.67 | 0.80 | 42 | 34W |
| 2 | 78 | 0.37 | 0.77 | 15 | empty |
| 3 | 51 | 0.29 | 0.75 | 11 | empty |
Compared structures
- 5VD2 · crystal structure of human WEE1 kinase domain in complex with PF-03814735 · the same entry in another collection · chain A against A, TM-score 1.00
- P30291 · AlphaFold monomer V2.0 prediction for WEE1-like protein kinase (P30291) · a predicted model of the same protein · chain A 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 P30291
- Elsewhere: RCSB PDB 5VD2 · PDBe 5VD2 · UniProt P30291
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