MolNFT v1 · #137046 · protein
Crystal structure of human WEE1 kinase domain in complex with pha- 848125
5VC6 · WEE1-like protein kinase: “Crystal structure of human WEE1 kinase domain in complex with pha- 848125”. X-ray diffraction, 1 ligand (P48), 4 pockets (best druggability 0.69). MolNFT v1 #137046 on GenesisL1: 3D structure, binding…
- PDB
- 5VC6
- Type
- protein
- Length
- 259 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
- P48
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | WEE1-like protein kinase (EC 2.7.10.2) | protein | 259 | 38% helix, 21% strand | P30291 |
Ligands and binding sites
- P48 · N,1,4,4-tetramethyl-8-{[4-(4-methylpiperazin-1-yl) phenyl]amino}-4,5-dihydro-1H-pyrazolo[4,3-h]quinazoline-3-carboxamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.69 | 0.81 | 47 | P48 |
| 2 | 87 | 0.35 | 0.74 | 15 | empty |
| 3 | 56 | 0.31 | 0.76 | 13 | empty |
| 4 | 52 | 0.28 | 0.75 | 13 | empty |
Compared structures
- 5VC6 · crystal structure of human WEE1 kinase domain in complex with PHA-848125 · 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 0.99
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 5VC6 · PDBe 5VC6 · UniProt P30291
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