MolNFT v1 · #143827 · protein
Lactate dehydrogenase in complex with inhibitor (R)-3-((2- CHLOROPHENYL)THIO)-6-(3-((4-FLUOROPHENYL)AMINO)PHENYL)-4-hydroxy-6- (thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one
6BB0 · L-lactate dehydrogenase a chain: “Lactate dehydrogenase in complex with inhibitor (R)-3-((2…”. X-ray diffraction, 4 ligands (NAD, D3S, LAC), 20 pockets (best druggability 0.89). MolNFT v1 #143827 on GenesisL1: 3D structure, binding…
- PDB
- 6BB0
- Type
- protein
- Length
- 1,299 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, D3S, LAC, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 323 | 46% helix, 20% strand | P00338 |
| B | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 324 | 45% helix, 19% strand | P00338 |
| C | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 325 | 46% helix, 18% strand | P00338 |
| D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 327 | 46% helix, 19% strand | P00338 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- D3S · (6S)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(2-hydroxyphenyl)-6-phenyl-5,6-dihydro-2H-pyran-2-one · ligand · 3 copies · chains A, C, D
- LAC · Lactic acid · ligand · chains B
- SO4 · Sulfate ion · ion · 4 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
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.89 | 0.91 | 119 | SO4 |
| 2 | 585 | 0.76 | 0.83 | 53 | NAD, D3S |
| 3 | 457 | 0.69 | 0.80 | 56 | NAD, LAC |
| 4 | 78 | 0.68 | 0.94 | 16 | empty |
| 5 | 70 | 0.67 | 0.94 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2939 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2915 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1681 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1677 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 971 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6BB0 · 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 6BB0 · PDBe 6BB0 · UniProt P00338
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