Research workbench
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
Analyse Lactate dehydrogenase in complex with inhibitor (R)-3-((2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BAD
- Type
- protein
- Length
- 1,324 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, D0Y, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 44% helix, 21% strand | P00338 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- D0Y · (6R)-3-[(2-chlorophenyl)sulfanyl]-6-{3-[(4-fluorophenyl)amino]phenyl}-4-hydroxy-6-(thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, C, B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 7 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.89 | 0.91 | 117 | SO4 |
| 2 | 527 | 0.79 | 0.86 | 59 | NAD, D0Y |
| 3 | 582 | 0.77 | 0.83 | 57 | NAD, EPE, D0Y |
| 4 | 577 | 0.77 | 0.83 | 56 | NAD, EPE, D0Y |
| 5 | 550 | 0.76 | 0.83 | 52 | NAD, EPE, D0Y |
Interfaces
6 interfaces between chains.
- C–D · 2941 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2902 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1716 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1637 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 983 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6BAD · 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 6BAD · PDBe 6BAD · UniProt P00338
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