Research workbench
Crystal structure of IDH1 R132H mutant in complex with compound 32
Analyse Crystal structure of IDH1 R132H mutant in complex with compound 32 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O2Z
- Type
- protein
- Length
- 822 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
- LJV, NAP
- Pockets
- 7 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 411 | 45% helix, 22% strand | O75874 |
Ligands and binding sites
- LJV · 6-{[(6-chloro-2-oxo-1,2-dihydroquinolin-3-yl) methyl]amino}-2-methylpyridine-3-carbonitrile · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.88 | 0.89 | 129 | LJV, NAP |
| 2 | 363 | 0.68 | 0.81 | 39 | empty |
| 3 | 270 | 0.62 | 0.80 | 35 | NAP |
| 4 | 274 | 0.61 | 0.79 | 39 | empty |
| 5 | 237 | 0.59 | 0.80 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 3120 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 6O2Z · Crystal structure of IDH1 R132H mutant in complex with compound 32 · 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 6O2Z · PDBe 6O2Z · UniProt O75874
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