Research workbench
Crystal structure of rabbit ldha in complex with a fragment inhibitor AP26256
Analyse Crystal structure of rabbit ldha in complex with a fragment inhibitor AP26256 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I9U
- Type
- protein
- Length
- 2,628 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase a chain
- EC
- 1.1.1.27
- UniProt
- P13491
- Ligands
- 1E7
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 323 | 45% helix, 21% strand | P13491 |
| B, C, D, E | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 44% helix, 21% strand | P13491 |
| F | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 329 | 44% helix, 19% strand | P13491 |
| G, H | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 326 | 45% helix, 19% strand | P13491 |
Ligands and binding sites
- 1E7 · 6-({2-[(5-chloro-2-methoxyphenyl)amino]-2-oxoethyl}sulfanyl)pyridine-3-carboxylic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.89 | 0.91 | 119 | empty |
| 2 | 759 | 0.87 | 0.90 | 84 | empty |
| 3 | 352 | 0.83 | 0.93 | 44 | empty |
| 4 | 893 | 0.83 | 0.85 | 88 | empty |
| 5 | 67 | 0.70 | 0.96 | 16 | empty |
Interfaces
14 interfaces between chains.
- B–D · 2922 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 2914 Ų buried · 29 hydrogen bonds · protein-protein
- E–G · 2908 Ų buried · 28 hydrogen bonds · protein-protein
- F–H · 2892 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1793 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4I9U · Crystal structure of rabbit LDHA in complex with a fragment inhibitor AP26256 · the same entry in another collection · chain H against H, TM-score 1.00
- P13491 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase a chain (P13491) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P13491
- Elsewhere: RCSB PDB 4I9U · PDBe 4I9U · UniProt P13491
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