MolNFT v1 · #82888 · protein
Human glyoxalase I with an N-hydroxypyridone derivative inhibitor
3W0T · Lactoylglutathione lyase: “Human glyoxalase I with an N-hydroxypyridone derivative inhibitor”. X-ray diffraction, 2 ligands (HPU, ZN), 9 pockets (best druggability 0.79). MolNFT v1 #82888 on GenesisL1: 3D structure, binding sites…
- PDB
- 3W0T
- Type
- protein
- Length
- 710 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactoylglutathione lyase
- EC
- 4.4.1.5
- UniProt
- Q04760
- Ligands
- HPU, ZN
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Lactoylglutathione lyase (EC 4.4.1.5) | protein | 176 | 30% helix, 29% strand | Q04760 |
| B | Lactoylglutathione lyase (EC 4.4.1.5) | protein | 182 | 27% helix, 28% strand | Q04760 |
Ligands and binding sites
- HPU · N-[3-(1-hydroxy-6-oxo-4-phenyl-1,6-dihydropyridin-2-yl)phenyl]methanesulfonamide · ligand · 4 copies · chains A, B, D, C
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.79 | 0.83 | 73 | EPE, HPU |
| 2 | 235 | 0.76 | 0.89 | 35 | HPU |
| 3 | 286 | 0.66 | 0.81 | 31 | HPU |
| 4 | 257 | 0.66 | 0.82 | 31 | HPU |
| 5 | 170 | 0.44 | 0.75 | 32 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3837 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 3693 Ų buried · 46 hydrogen bonds · protein-protein
- B–D · 419 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 161 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 102 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3W0T · Human Glyoxalase I with an N-hydroxypyridone derivative inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q04760 · AlphaFold monomer V2.0 prediction for lactoylglutathione lyase (Q04760) · 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 Q04760
- Elsewhere: RCSB PDB 3W0T · PDBe 3W0T · UniProt Q04760
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