MolNFT v1 · #143828 · protein
Lactate dehydrogenase in complex with inhibitor (R)-5-((2- CHLOROPHENYL)THIO)-6'-(4-fluorophenoxy)-4-hydroxy-2-(thiophen-3-yl)- 2,3-dihydro-[2,2'-bipyridin]-6(1H)-one
6BB1 · L-lactate dehydrogenase a chain: “Lactate dehydrogenase in complex with inhibitor (R)-5-((2…”. X-ray diffraction, 4 ligands (NAD, D3J, LAC), 20 pockets (best druggability 0.89). MolNFT v1 #143828 on GenesisL1: 3D structure, binding…
- PDB
- 6BB1
- Type
- protein
- Length
- 2,577 residues
- Chains
- 8
- 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
- NAD, D3J, LAC, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 8 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 323 | 45% helix, 21% strand | P00338 |
| B | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 322 | 44% helix, 21% strand | P00338 |
| C | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 328 | 45% helix, 21% strand | P00338 |
| D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 329 | 45% helix, 21% strand | P00338 |
| E | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 310 | 46% helix, 22% strand | P00338 |
| F | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 314 | 46% helix, 22% strand | P00338 |
| G | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 322 | 46% helix, 22% strand | P00338 |
| H | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 329 | 44% helix, 21% strand | P00338 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- D3J · (2R)-5-[(2-chlorophenyl)sulfanyl]-6'-(4-fluorophenoxy)-4-hydroxy-2-(thiophen-3-yl)-2,3-dihydro[2,2'-bipyridin]-6(1H)-one · ligand · 6 copies · chains A, B, D, E, F, G
- LAC · Lactic acid · ligand · chains C
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, B, D, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.89 | 0.91 | 122 | SO4 |
| 2 | 1125 | 0.89 | 0.91 | 121 | empty |
| 3 | 758 | 0.74 | 0.79 | 58 | NAD, D3J |
| 4 | 697 | 0.71 | 0.78 | 57 | NAD, D3J |
| 5 | 71 | 0.71 | 0.97 | 18 | empty |
Interfaces
13 interfaces between chains.
- G–H · 2916 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2899 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2892 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 2839 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1643 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6BB1 · Lactate Dehydrogenase in complex with inhibitor… · 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 6BB1 · PDBe 6BB1 · UniProt P00338
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