MolNFT v1 · #86222 · protein
Co-crystal structure of wbdd and kinase inhibitor LY294002.
4AZT · Methyltransferase wbdd: “Co-crystal structure of wbdd and kinase inhibitor LY294002.”. X-ray diffraction, 4 ligands (SAM, LY2, SO4), 3 pockets (best druggability 0.66). MolNFT v1 #86222 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4AZT
- Type
- protein
- Length
- 435 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase wbdd
- UniProt
- Q47592
- Ligands
- SAM, LY2, SO4, CL
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyltransferase wbdd | protein | 435 | 42% helix, 21% strand | Q47592 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- LY2 · 2-morpholin-4-yl-7-phenyl-4H-chromen-4-one · ligand · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A
- CL · Chloride ion · ion · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.66 | 0.83 | 36 | SAM |
| 2 | 194 | 0.56 | 0.79 | 28 | LY2 |
| 3 | 70 | 0.39 | 0.79 | 21 | empty |
Compared structures
- 4AZT · Co-crystal structure of WbdD and kinase inhibitor LY294002. · the same entry in another collection · chain A against A, TM-score 1.00
- Q47592 · AlphaFold monomer V2.0 prediction for O-antigen chain terminator bifunctional… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q47592
- Elsewhere: RCSB PDB 4AZT · PDBe 4AZT · UniProt Q47592
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