MolNFT v1 · #137081 · protein
Crystal structure of human WEE1 kinase domain in complex with rac-IV- 050, a MK1775 analougue
5VD5 · WEE1-like protein kinase: “Crystal structure of human WEE1 kinase domain in complex with rac-IV- 050, a MK1775 analougue”. X-ray diffraction, 2 ligands (99M, CL), 3 pockets (best druggability 0.72). MolNFT v1 #137081 on GenesisL1…
- PDB
- 5VD5
- Type
- protein
- Length
- 260 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
- 99M, CL
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | WEE1-like protein kinase (EC 2.7.10.2) | protein | 260 | 39% helix, 21% strand | P30291 |
Ligands and binding sites
- 99M · 1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-6-{[4-(morpholin-4-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one · ligand · chains A
- CL · Chloride 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 | 461 | 0.72 | 0.81 | 58 | 99M |
| 2 | 83 | 0.37 | 0.76 | 15 | empty |
| 3 | 58 | 0.28 | 0.74 | 12 | empty |
Compared structures
- 5VD5 · CRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH RAC-IV-050, 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 5VD5 · PDBe 5VD5 · UniProt P30291
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