Research workbench
Lactate dehydrogenase a in complex with inhibitor compound 22
Analyse Lactate dehydrogenase a in complex with inhibitor compound 22 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JNK
- Type
- protein
- Length
- 1,319 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, ZHK, LAC, SO4
- Pockets
- 18 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 326 | 47% helix, 19% strand | P00338 |
| 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
- ZHK · (2R)-2-{[5-cyano-4-(3,4-dichlorophenyl)-6-oxo-1,6-dihydropyrimidin-2-yl]sulfanyl}-N-(4-sulfamoylphenyl)propanamide · 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
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.89 | 0.91 | 119 | SO4 |
| 2 | 856 | 0.75 | 0.79 | 73 | NAI, ZHK |
| 3 | 526 | 0.72 | 0.81 | 57 | NAI, ZHK |
| 4 | 658 | 0.71 | 0.78 | 55 | NAI, ZHK |
| 5 | 231 | 0.69 | 0.86 | 39 | NAI, LAC |
Interfaces
6 interfaces between chains.
- C–D · 2956 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2876 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1773 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1679 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 959 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4JNK · Lactate Dehydrogenase A in complex with inhibitor compound 22 · 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 4JNK · PDBe 4JNK · UniProt P00338
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