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Crystal structure of human cytosolic isocitrate dehydrogenase (IDH1) R132H mutant in complex with NADPH and ag-881 (vorasidenib) inhibitor
Analyse Crystal structure of human cytosolic isocitrate dehydrogenase (IDH1) R132H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VEI
- Type
- protein
- Length
- 830 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
- NDP, 33O, 9UO, MLT, SO4
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 413 | 48% helix, 22% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 417 | 48% helix, 22% strand | O75874 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 33O · 3,6,9,12,15,18,21,24,27,30,33,36-dodecaoxaoctatriacontane-1,38-diol · ligand · chains A
- 9UO · 6-(6-chloropyridin-2-yl)-N2,N4-bis[(2R)-1,1,1-trifluoropropan-2-yl]-1,3,5-triazine-2,4-diamine · ligand · chains A, B
- MLT · D-malate · ligand · chains A, B
- SO4 · Sulfate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · chains A
- MLA · Malonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.81 | 0.97 | 30 | 9UO |
| 2 | 934 | 0.81 | 0.83 | 84 | PEG, NDP |
| 3 | 318 | 0.57 | 0.76 | 37 | empty |
| 4 | 168 | 0.56 | 0.81 | 29 | PEG |
| 5 | 74 | 0.48 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3542 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 6VEI · Crystal Structure of Human Cytosolic Isocitrate Dehydrogenase (IDH1) R132H Mutant in… · 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 6VEI · PDBe 6VEI · UniProt O75874
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