MolNFT v1 · #137093 · protein
Crystal structure of human WEE2 kinase domain in complex with MK1775
5VDK · WEE1-like protein kinase 2: “Crystal structure of human WEE2 kinase domain in complex with MK1775”. X-ray diffraction, 2 ligands (8X7, PO4), 1 pocket (best druggability 0.67). MolNFT v1 #137093 on GenesisL1: 3D structure, binding…
- PDB
- 5VDK
- Type
- protein
- Length
- 260 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- WEE1-like protein kinase 2
- EC
- 2.7.10.2
- UniProt
- P0C1S8
- Ligands
- 8X7, PO4
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | WEE1-like protein kinase 2 (EC 2.7.10.2) | protein | 260 | 37% helix, 20% strand | P0C1S8 |
Ligands and binding sites
- 8X7 · 1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one · ligand · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.67 | 0.85 | 27 | 8X7, PO4 |
Compared structures
- 5VDK · Crystal structure of human WEE2 kinase domain in complex with MK1775 · the same entry in another collection · chain A against A, TM-score 1.00
- P0C1S8 · AlphaFold monomer V2.0 prediction for WEE1-like protein kinase 2 (P0C1S8) · 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 P0C1S8
- Elsewhere: RCSB PDB 5VDK · PDBe 5VDK · UniProt P0C1S8
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