Research workbench
Lactate dehydrogenase in complex with inhibitor 3-((2-chlorophenyl) thio)-6-(6-((4-FLUOROPHENYL)AMINO)PYRIDIN-2-yl)-4-hydroxy-6- (thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one
Analyse Lactate dehydrogenase in complex with inhibitor 3-((2-chlorophenyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BB3
- Type
- protein
- Length
- 1,301 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, D4A, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 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 | 331 | 44% helix, 21% strand | P00338 |
| B | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 322 | 45% helix, 21% strand | P00338 |
| C | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 324 | 45% helix, 21% strand | P00338 |
| D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 324 | 44% helix, 21% strand | P00338 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- D4A · (6R)-3-[(2-chlorophenyl)sulfanyl]-6-{6-[(4-fluorophenyl)amino]pyridin-2-yl}-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 · 7 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.89 | 0.91 | 115 | SO4 |
| 2 | 755 | 0.75 | 0.80 | 56 | NAD, D4A |
| 3 | 578 | 0.71 | 0.79 | 58 | NAD, D4A |
| 4 | 456 | 0.69 | 0.80 | 54 | NAD, D4A |
| 5 | 65 | 0.68 | 0.96 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2947 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2936 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1699 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1593 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 969 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6BB3 · 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 6BB3 · PDBe 6BB3 · UniProt P00338
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