MolNFT v1 · #161185 · protein
Crystal structure of IDH1 R132H in complex with HMS101
6Q6F · Isocitrate dehydrogenase [NADP] cytoplasmic: “Crystal structure of IDH1 R132H in complex with HMS101”. X-ray diffraction, 1 ligand (HJQ), 11 pockets (best druggability 0.81). MolNFT v1 #161185 on GenesisL1: 3D structure, binding…
- PDB
- 6Q6F
- Type
- protein
- Length
- 811 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
- HJQ
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 402 | 43% helix, 19% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 409 | 44% helix, 19% strand | O75874 |
Ligands and binding sites
- HJQ · (2~{R})-2-[2-[(3~{R})-3-(4-fluorophenyl)pyrrolidin-1-yl]ethyl]-1,4-dimethyl-piperazine · ligand · 2 copies · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.81 | 0.87 | 71 | HJQ |
| 2 | 653 | 0.79 | 0.84 | 80 | empty |
| 3 | 155 | 0.63 | 0.85 | 27 | empty |
| 4 | 256 | 0.61 | 0.80 | 40 | empty |
| 5 | 115 | 0.54 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2523 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 6Q6F · Crystal structure of IDH1 R132H in complex with HMS101 · 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 6Q6F · PDBe 6Q6F · UniProt O75874
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