MolNFT v1 · #137080 · protein
Crystal structure of human WEE1 kinase domain in complex with rac-IV- 016, a MK1775 analougue
5VD4 · WEE1-like protein kinase: “Crystal structure of human WEE1 kinase domain in complex with rac-IV- 016, a MK1775 analougue”. X-ray diffraction, 3 ligands (99J, PO4, CL), 4 pockets (best druggability 0.62). MolNFT v1 #137080 on…
- PDB
- 5VD4
- Type
- protein
- Length
- 261 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
- 99J, PO4, CL
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | WEE1-like protein kinase (EC 2.7.10.2) | protein | 261 | 41% helix, 21% strand | P30291 |
Ligands and binding sites
- 99J · 6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1-{6-[(1S)-2,2,2-trifluoro-1-hydroxyethyl]pyridin-2-yl}-1,2-dihydro-3H-pyrazolo[3, 4-d]pyrimidin-3-one · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · 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 | 319 | 0.62 | 0.79 | 37 | 99J |
| 2 | 78 | 0.36 | 0.76 | 14 | EDO |
| 3 | 60 | 0.32 | 0.76 | 13 | empty |
| 4 | 72 | 0.31 | 0.74 | 12 | empty |
Compared structures
- 5VD4 · CRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH RAC-IV-016, a MK1775… · 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 5VD4 · PDBe 5VD4 · UniProt P30291
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