MolNFT v1 · #143826 · protein
Lactate dehydrogenase in complex with inhibitor (S)-5-((2- CHLOROPHENYL)THIO)-6'-((4-FLUOROPHENYL)AMINO)-4-hydroxy-2-(thiophen- 3-yl)-2,3-dihydro-[2,2'-bipyridin]-6(1H)-one
6BAZ · L-lactate dehydrogenase a chain: “Lactate dehydrogenase in complex with inhibitor (S)-5-((2…”. X-ray diffraction, 4 ligands (NAD, D47, LAC), 19 pockets (best druggability 0.89). MolNFT v1 #143826 on GenesisL1: 3D structure, binding…
- PDB
- 6BAZ
- Type
- protein
- Length
- 1,307 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
- NAD, D47, LAC, SO4
- Pockets
- 19 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 325 | 44% helix, 22% strand | P00338 |
| B | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 323 | 45% helix, 19% 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 | 331 | 43% helix, 21% strand | P00338 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- D47 · (3S,6S)-3-[(2-chlorophenyl)sulfanyl]-6-{6-[(4-fluorophenyl)amino]pyridin-2-yl}-6-(thiophen-3-yl) piperidine-2,4-dione · ligand · 2 copies · chains C, D
- LAC · Lactic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, C, B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, C
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 | 1122 | 0.89 | 0.91 | 114 | SO4 |
| 2 | 688 | 0.79 | 0.83 | 72 | NAD, D47 |
| 3 | 585 | 0.73 | 0.81 | 62 | NAD, D47 |
| 4 | 508 | 0.72 | 0.81 | 59 | NAD, LAC |
| 5 | 88 | 0.72 | 0.95 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2975 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2933 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1769 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1727 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 997 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6BAZ · 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 6BAZ · PDBe 6BAZ · UniProt P00338
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