Research workbench
Lactate dehydrogenase in complex with hydroxylactam inhibitor compound 9: (6R)-3-[(2-CHLOROPHENYL)SULFANYL]-4-hydroxy-6-(3-hydroxyphenyl)-6- (thiophen-3-yl)-5,6-dihydropyridin-2(1H)-one
Analyse Lactate dehydrogenase in complex with hydroxylactam inhibitor compound 9… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IXS
- Type
- protein
- Length
- 1,305 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
- 6EY, TXD, NAI, SO4
- Pockets
- 18 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 327 | 45% helix, 21% strand | P00338 |
| B, C | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 324 | 46% helix, 19% strand | P00338 |
| D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 330 | 45% helix, 18% strand | P00338 |
Ligands and binding sites
- 6EY · (6R)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(3-hydroxyphenyl)-6-(thiophen-3-yl)-5,6-dihydropyridin-2(1H)-one · ligand · 4 copies · chains A, B, C, D
- TXD · 1,4,5,6-tetrahydronicotinamide adenine dinucleotide · ligand · 3 copies · chains A, B, D
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains C
- 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
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.89 | 0.91 | 119 | SO4 |
| 2 | 724 | 0.79 | 0.83 | 71 | TXD, 6EY |
| 3 | 567 | 0.75 | 0.82 | 52 | TXD, 6EY |
| 4 | 539 | 0.71 | 0.79 | 55 | NAI, 6EY |
| 5 | 513 | 0.71 | 0.80 | 55 | TXD, 6EY |
Interfaces
6 interfaces between chains.
- C–D · 2922 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2889 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1713 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1675 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 949 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5IXS · Lactate Dehydrogenase in complex with hydroxylactam inhibitor compound 9… · 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 5IXS · PDBe 5IXS · UniProt P00338
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