Research workbench
Lactate dehydrogenase in complex with inhibitor compound 47
Analyse Lactate dehydrogenase in complex with inhibitor compound 47 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RLS
- Type
- protein
- Length
- 1,310 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, 2OP, 49C, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 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 | 331 | 45% helix, 18% strand | P00338 |
| B | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 324 | 46% helix, 19% strand | P00338 |
| C | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 327 | 46% helix, 19% strand | P00338 |
| D | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 328 | 45% helix, 19% strand | P00338 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- 2OP · (2S)-2-hydroxypropanoic acid · ligand · 2 copies · chains B, C
- 49C · (1R)-5'-[(2-chlorophenyl)sulfanyl]-4'-hydroxy-2,3-dihydrospiro[indene-1,2'-pyran]-6'(3'H)-one · ligand · chains D
- SO4 · Sulfate ion · ion · 2 copies · chains A, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.82 | 0.93 | 44 | empty |
| 2 | 290 | 0.82 | 0.93 | 38 | SO4 |
| 3 | 590 | 0.77 | 0.84 | 59 | NAI, 49C |
| 4 | 83 | 0.70 | 0.95 | 16 | empty |
| 5 | 476 | 0.70 | 0.80 | 55 | NAI, 2OP |
Interfaces
6 interfaces between chains.
- C–D · 2902 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2864 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1761 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1684 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 962 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4RLS · Lactate Dehydrogenase in complex with inhibitor compound 47 · 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 4RLS · PDBe 4RLS · UniProt P00338
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