MolNFT v1 · #122726 · protein
Lactate dehydrogenase in complex with hydroxylactam inhibitor compound 31: (2~{S})-5-(2-CHLOROPHENYL)SULFANYL-2-(4-morpholin-4-ylphenyl)-4- oxidanyl-2-thiophen-3-yl-1,3-dihydropyridin-6-one
5IXY · L-lactate dehydrogenase a chain: “Lactate dehydrogenase in complex with hydroxylactam inhibitor compound 31…”. X-ray diffraction, 3 ligands (NAD, GN2, SO4), 19 pockets (best druggability 0.89). MolNFT v1 #122726 on GenesisL1: 3D…
- PDB
- 5IXY
- Type
- protein
- Length
- 1,321 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, GN2, SO4
- Pockets
- 19 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 44% helix, 21% strand | P00338 |
| D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 328 | 43% helix, 21% strand | P00338 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- GN2 · (2~{S})-5-(2-chlorophenyl)sulfanyl-2-(4-morpholin-4-ylphenyl)-4-oxidanyl-2-thiophen-3-yl-1,3-dihydropyridin-6-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
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.89 | 0.91 | 110 | SO4 |
| 2 | 742 | 0.72 | 0.78 | 57 | NAD, GN2 |
| 3 | 87 | 0.72 | 0.95 | 17 | empty |
| 4 | 681 | 0.71 | 0.78 | 55 | NAD, GN2 |
| 5 | 627 | 0.70 | 0.78 | 57 | NAD, GN2 |
Interfaces
6 interfaces between chains.
- C–D · 2996 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2970 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1754 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 1719 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 963 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5IXY · Lactate Dehydrogenase in complex with hydroxylactam inhibitor compound 31… · 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 5IXY · PDBe 5IXY · UniProt P00338
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