MolNFT v1 · #81136 · protein
Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase in complex with inhibitor
3UHM: “Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase in complex with inhibitor”. X-ray diffraction, 3 ligands (RFN, GAI, ZN), 3 pockets (best druggability 0.70). MolNFT v1 #81136 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3UHM
- Type
- protein
- Length
- 299 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
- EC
- 3.5.1.-
- UniProt
- P47205
- Ligands
- RFN, GAI, ZN
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 299 | 26% helix, 34% strand | P47205 |
Ligands and binding sites
- RFN · (2R)-N-hydroxy-2-methyl-2-(methylsulfonyl)-4-(2-oxo-4-phenylpyridin-1(2H)-yl)butanamide · ligand · chains A
- GAI · Guanidine · ligand · chains A
- ZN · Zinc ion · metal · 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
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 | 413 | 0.70 | 0.81 | 44 | RFN, GAI, EDO |
| 2 | 76 | 0.55 | 0.86 | 20 | empty |
| 3 | 70 | 0.36 | 0.77 | 14 | empty |
Compared structures
- 3UHM · UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase in complex with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P47205 · AlphaFold monomer V2.0 prediction for udp-3-O-acyl-N- acetylglucosamine deacetylase… · 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 P47205
- Elsewhere: RCSB PDB 3UHM · PDBe 3UHM · UniProt P47205
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