Research workbench
Novel modes of inhibition of wild-type IDH1: direct covalent modification of HIS315 with CMPD1
Analyse Novel modes of inhibition of wild-type IDH1: direct covalent modification of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BKX
- Type
- protein
- Length
- 1,247 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
- ICT, DWP, CA
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 417 | 49% helix, 20% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 416 | 48% helix, 22% strand | O75874 |
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 414 | 48% helix, 22% strand | O75874 |
Ligands and binding sites
- ICT · Isocitric acid · ligand · 3 copies · chains C, B, A
- DWP · (6aS,7S,9R,10aS)-7,10a-dimethyl-8-oxo-2-(phenylamino)-5,6,6a,7,8,9,10,10a-octahydrobenzo[h]quinazoline-9-carbonitrile · ligand · 3 copies · chains C, B, A
- CA · Calcium ion · metal · 3 copies · chains C, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.76 | 0.79 | 68 | ICT, DWP, CA |
| 2 | 858 | 0.74 | 0.78 | 62 | ICT, DWP |
| 3 | 713 | 0.70 | 0.77 | 71 | empty |
| 4 | 277 | 0.59 | 0.78 | 32 | empty |
| 5 | 251 | 0.52 | 0.76 | 29 | empty |
Interfaces
3 interfaces between chains.
- B–A · 3661 Ų buried · 57 hydrogen bonds · protein-protein
- C–B · 245 Ų buried · 2 hydrogen bonds · protein-protein
- C–A · 215 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6BKX · Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of His315 with… · the same entry in another collection · chain C against C, 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 6BKX · PDBe 6BKX · UniProt O75874
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