MolNFT v1 · #105481 · protein
Lactate dehydrogenase in complex with inhibitor compound 31
4R68 · L-lactate dehydrogenase a chain: “Lactate dehydrogenase in complex with inhibitor compound 31”. X-ray diffraction, 3 ligands (NAI, W31, SO4), 19 pockets (best druggability 0.89). MolNFT v1 #105481 on GenesisL1: 3D structure, binding…
- PDB
- 4R68
- Type
- protein
- Length
- 1,316 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase a chain
- EC
- 1.1.1.27
- UniProt
- P00338
- Ligands
- NAI, W31, SO4
- Pockets
- 19 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 44% helix, 21% strand | P00338 |
| C | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 323 | 46% helix, 20% strand | P00338 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- W31 · (1S)-1-phenylethyl (4-chloro-3-{[(4S)-4-(2,6-dichlorophenyl)-2-hydroxy-6-oxocyclohex-1-en-1-yl]sulfanyl}phenyl)acetate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.89 | 0.91 | 123 | SO4 |
| 2 | 811 | 0.77 | 0.80 | 74 | NAI, W31 |
| 3 | 769 | 0.76 | 0.80 | 57 | NAI, W31 |
| 4 | 738 | 0.73 | 0.79 | 70 | NAI, W31 |
| 5 | 67 | 0.66 | 0.94 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2929 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2905 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1725 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1677 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 934 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4R68 · Lactate Dehydrogenase in complex with inhibitor compound 31 · the same entry in another collection · chain A against A, TM-score 1.00
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 P00338
- Elsewhere: RCSB PDB 4R68 · PDBe 4R68 · UniProt P00338
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.