Research workbench
Novel modes of inhibition of wild-type IDH1:DIRECT covalent modification of HIS315 with CMPD11
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
- 6BL0
- Type
- protein
- Length
- 1,248 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, NAP, DWJ, MG
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 416 | 48% helix, 22% strand | O75874 |
Ligands and binding sites
- ICT · Isocitric acid · ligand · 3 copies · chains A, B, C
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B, C
- DWJ · (5aS,6S,8S,9aS)-2-(benzenecarbonyl)-6-methyl-7-oxo-9a-phenyl-4,5,5a,6,7,8,9,9a-octahydro-2H-benzo[g]indazole-8-carbonitrile · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.79 | 0.81 | 92 | ICT, NAP |
| 2 | 863 | 0.74 | 0.79 | 63 | MG, ICT, DWJ |
| 3 | 698 | 0.70 | 0.77 | 64 | empty |
| 4 | 375 | 0.58 | 0.76 | 55 | MG, ICT, NAP |
| 5 | 224 | 0.53 | 0.77 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3675 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 268 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 242 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6BL0 · Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of His315 with… · 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 6BL0 · PDBe 6BL0 · UniProt O75874
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