Research workbench
Human IDH1 R132C mutant complexed with compound a.
Analyse Human IDH1 R132C mutant complexed with compound a. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IO0
- Type
- protein
- Length
- 800 residues
- Chains
- 2
- 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
- AOU, NDP
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 400 | 47% helix, 23% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 400 | 47% helix, 24% strand | O75874 |
Ligands and binding sites
- AOU · (2E)-3-{3-[3-(2,6-dichlorophenyl)-5-(propan-2-yl)-1,2-oxazole-4-carbonyl]-1-methyl-1H-indol-7-yl}prop-2-enoic acid · ligand · 2 copies · chains A, B
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- CIT · Citric acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.85 | 0.85 | 123 | AOU, NDP |
| 2 | 330 | 0.79 | 0.89 | 36 | AOU |
| 3 | 235 | 0.58 | 0.79 | 32 | empty |
| 4 | 146 | 0.53 | 0.80 | 25 | empty |
| 5 | 79 | 0.43 | 0.81 | 19 | CIT |
Interfaces
1 interface between chains.
- A–B · 2577 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 6IO0 · Human IDH1 R132C mutant complexed with compound A. · 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 O75874
- Elsewhere: RCSB PDB 6IO0 · PDBe 6IO0 · UniProt O75874
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