MolNFT v1 · #138102 · protein
Crystal structure of lactate dehydrogenase a in complex with inhibitor compound 11
5W8H · L-lactate dehydrogenase a chain: “Crystal structure of lactate dehydrogenase a in complex with inhibitor compound 11”. X-ray diffraction, 1 ligand (9Y1), 18 pockets (best druggability 0.89). MolNFT v1 #138102 on GenesisL1: 3D…
- PDB
- 5W8H
- Type
- protein
- Length
- 1,320 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
- 9Y1
- Pockets
- 18 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 45% helix, 18% strand | P00338 |
| C, D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 329 | 46% helix, 19% strand | P00338 |
Ligands and binding sites
- 9Y1 · 2-[3-(4-fluorophenyl)-5-(trifluoromethyl)-1H-pyrazol-1-yl]-1,3-thiazole-4-carboxylic acid · ligand · 7 copies · chains A, B, C
- ACT · Acetate ion · additive · 4 copies · chains A, C, B, D
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, C, B, D
- GOL · Glycerol · additive · 2 copies · chains A, C, B, D
- MLA · Malonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.89 | 0.91 | 124 | ACT, DMS |
| 2 | 212 | 0.68 | 0.86 | 41 | MLA |
| 3 | 502 | 0.66 | 0.78 | 54 | 9Y1 |
| 4 | 65 | 0.66 | 0.94 | 16 | empty |
| 5 | 461 | 0.66 | 0.78 | 48 | 9Y1 |
Interfaces
6 interfaces between chains.
- C–D · 2929 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2864 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1632 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1607 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 949 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5W8H · Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 11 · 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 5W8H · PDBe 5W8H · UniProt P00338
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