MolNFT v1 · #125305 · protein
Crystal structure of iso-citrate dehydrogenase R132H in complex with a novel inhibitor (compound 13A)
5L57 · Isocitrate dehydrogenase [NADP] cytoplasmic: “Crystal structure of iso-citrate dehydrogenase R132H in complex with a novel inhibitor (compound 13A)”. X-ray diffraction, 2 ligands (NDP, 6N3), 7 pockets (best druggability 0.69).…
- PDB
- 5L57
- Type
- protein
- Length
- 409 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP] cytoplasmic
- EC
- 1.1.1.42
- UniProt
- O75874
- Ligands
- NDP, 6N3
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 409 | 44% helix, 17% strand | O75874 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- 6N3 · (1~{R},5~{S})-3-[6-(3-methylbutoxy)-5-[[(1~{R},3~{S})-5-oxidanyl-2-adamantyl]carbamoyl]pyridin-2-yl]-3-azabicyclo[3.1.0]hexane-6-carboxylic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.69 | 0.82 | 41 | 6N3 |
| 2 | 272 | 0.61 | 0.80 | 41 | empty |
| 3 | 82 | 0.50 | 0.84 | 21 | empty |
| 4 | 62 | 0.46 | 0.84 | 19 | empty |
| 5 | 149 | 0.44 | 0.76 | 24 | empty |
Compared structures
- 5L57 · Crystal structure of Iso-citrate Dehydrogenase R132H in complex with a novel inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- O75874 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] cytoplasmic (O75874) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 O75874
- Elsewhere: RCSB PDB 5L57 · PDBe 5L57 · UniProt O75874
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