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Lactate dehydrogenase a in complex with a substituted pyrazine inhibitor compound 18
Analyse Lactate dehydrogenase a in complex with a substituted pyrazine inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M49
- 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
- NAI, 22Y, LAC, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% 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 | 45% helix, 19% strand | P00338 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- 22Y · 3-(5-amino-6-{[(1R)-1-phenylethyl]amino}pyrazin-2-yl)-4-chlorobenzoic acid · ligand · 3 copies · chains A, C, D
- LAC · Lactic acid · ligand · chains B
- SO4 · Sulfate ion · ion · 3 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.89 | 0.91 | 134 | SO4 |
| 2 | 649 | 0.71 | 0.78 | 60 | NAI, 22Y |
| 3 | 235 | 0.70 | 0.86 | 40 | NAI, LAC |
| 4 | 557 | 0.69 | 0.78 | 53 | NAI, 22Y |
| 5 | 592 | 0.69 | 0.78 | 58 | NAI, 22Y |
Interfaces
6 interfaces between chains.
- C–D · 2948 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2895 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1737 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1698 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 971 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4M49 · Lactate Dehydrogenase A in complex with a substituted pyrazine inhibitor compound 18 · 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 4M49 · PDBe 4M49 · UniProt P00338
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