Research workbench
Crystal structure of IDH1 R132H mutant in complex with compound 24
Analyse Crystal structure of IDH1 R132H mutant in complex with compound 24 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O2Y
- Type
- protein
- Length
- 1,233 residues
- Chains
- 3
- 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
- LJY, NAP
- Pockets
- 14 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 413 | 47% helix, 22% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 411 | 46% helix, 22% strand | O75874 |
| C | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 409 | 48% helix, 14% strand | O75874 |
Ligands and binding sites
- LJY · 4-{[(6-chloro-2-oxo-1,2-dihydroquinolin-3-yl) methyl]amino}-2-methoxybenzonitrile · ligand · 3 copies · chains A, B, C
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, C
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.89 | 0.93 | 79 | LJY, BME |
| 2 | 849 | 0.78 | 0.81 | 94 | empty |
| 3 | 230 | 0.72 | 0.87 | 33 | LJY |
| 4 | 426 | 0.68 | 0.80 | 48 | NAP |
| 5 | 238 | 0.66 | 0.84 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3075 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 434 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 103 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6O2Y · Crystal structure of IDH1 R132H mutant in complex with compound 24 · 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 6O2Y · PDBe 6O2Y · UniProt O75874
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