MolNFT v1 · #94868 · protein
Crystal structure of rabbit ldha in complex with AP28669
4I9H · L-lactate dehydrogenase a chain: “Crystal structure of rabbit ldha in complex with AP28669”. X-ray diffraction, 1 ligand (1E4), 20 pockets (best druggability 0.89). MolNFT v1 #94868 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4I9H
- Type
- protein
- Length
- 2,624 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
- 1E4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 325 | 45% helix, 19% strand | P13491 |
| B | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 327 | 45% helix, 19% strand | P13491 |
| C | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 328 | 46% helix, 19% strand | P13491 |
| D, E | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 331 | 46% helix, 19% strand | P13491 |
| F | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 329 | 46% helix, 19% strand | P13491 |
| G | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 324 | 45% helix, 19% strand | P13491 |
| H | L-lactate dehydrogenase a chain (EC 1.1.1.27) | protein | 329 | 45% helix, 19% strand | P13491 |
Ligands and binding sites
- 1E4 · 1-O-[3-(5-carboxypyridin-2-yl)-5-fluorophenyl]-6-O-[4-({[(5-carboxypyridin-2-yl)sulfanyl]acetyl}amino)-2-chloro-5-methoxyphenyl]-D-mannitol · 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 | 1156 | 0.89 | 0.91 | 123 | empty |
| 2 | 857 | 0.88 | 0.90 | 86 | empty |
| 3 | 346 | 0.83 | 0.92 | 45 | empty |
| 4 | 1178 | 0.81 | 0.82 | 98 | empty |
| 5 | 70 | 0.71 | 0.96 | 15 | empty |
Interfaces
13 interfaces between chains.
- E–G · 2898 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 2884 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 2862 Ų buried · 27 hydrogen bonds · protein-protein
- F–H · 2857 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1777 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
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 4I9H · PDBe 4I9H · UniProt P13491
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