Research workbench
Novel binding modes of inhibition of wild-type IDH1: allosteric inhibition with CMPD2
Analyse Novel binding modes of inhibition of wild-type IDH1: allosteric inhibition with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BKY
- Type
- protein
- Length
- 2,488 residues
- Chains
- 6
- 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
- LMR, K32, MG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, E | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 416 | 48% helix, 22% strand | O75874 |
| C | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 414 | 48% helix, 22% strand | O75874 |
| F, B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 413 | 48% helix, 22% strand | O75874 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · 3 copies · chains D, C, F, E, A, B
- K32 · 4,5,6,7-tetrabromo-1H,3H-benzimidazol-2-one · ligand · 3 copies · chains D, C, A, B, F, E
- MG · Magnesium ion · metal · 4 copies · chains D, C, F, E, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.76 | 0.79 | 94 | LMR, MG |
| 2 | 88 | 0.75 | 0.97 | 20 | K32 |
| 3 | 908 | 0.75 | 0.79 | 78 | empty |
| 4 | 83 | 0.75 | 0.97 | 23 | K32 |
| 5 | 915 | 0.75 | 0.78 | 78 | LMR, MG |
Interfaces
7 interfaces between chains.
- D–C · 3464 Ų buried · 56 hydrogen bonds · protein-protein
- F–E · 3456 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 3454 Ų buried · 52 hydrogen bonds · protein-protein
- D–F · 306 Ų buried · 4 hydrogen bonds · protein-protein
- C–A · 302 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6BKY · Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with Cmpd2 · the same entry in another collection · chain D against D, 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 6BKY · PDBe 6BKY · UniProt O75874
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