Research workbench
Novel modes of inhibition of wild-type IDH1: direct covalent modification of HIS315 with CMPD13
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
- 6BL1
- 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, DWG, CA
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 416 | 47% helix, 22% strand | O75874 |
Ligands and binding sites
- ICT · Isocitric acid · ligand · 3 copies · chains B, A, C
- DWG · (6aS,7S,9S,10aS)-7-methyl-8-oxo-10a-phenyl-2-(phenylamino)-5,6,6a,7,8,9,10,10a-octahydrobenzo[h]quinazoline-9-carbonitrile · ligand · 3 copies · chains B, C, A
- CA · Calcium ion · metal · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.75 | 0.79 | 62 | ICT, DWG |
| 2 | 823 | 0.74 | 0.78 | 66 | CA, ICT, DWG |
| 3 | 238 | 0.49 | 0.74 | 28 | empty |
| 4 | 149 | 0.49 | 0.78 | 21 | empty |
| 5 | 202 | 0.49 | 0.76 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–A · 3616 Ų buried · 61 hydrogen bonds · protein-protein
- B–C · 182 Ų buried · 2 hydrogen bonds · protein-protein
- C–A · 29 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6BL1 · Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of His315 with… · the same entry in another collection · chain B against B, 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 6BL1 · PDBe 6BL1 · UniProt O75874
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