MolNFT v1 · #167280 · protein
Crystal structure of human mitochondrial isocitrate dehydrogenase (IDH2) R140Q mutant homodimer in complex with NADPH and ag-881 (vorasidenib) inhibitor.
6VFZ · Isocitrate dehydrogenase [NADP], mitochondrial: “Crystal structure of human mitochondrial isocitrate dehydrogenase (IDH2) R140Q mutant homodimer in complex…”. X-ray diffraction, 4 ligands (NDP, 9UO, CA), 9 pockets (best druggability…
- PDB
- 6VFZ
- Type
- protein
- Length
- 822 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP], mitochondrial
- EC
- 1.1.1.42
- UniProt
- P48735
- Ligands
- NDP, 9UO, CA, NA
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP], mitochondrial (EC 1.1.1.42) | protein | 416 | 48% helix, 21% strand | P48735 |
| B | Isocitrate dehydrogenase [NADP], mitochondrial (EC 1.1.1.42) | protein | 406 | 47% helix, 22% strand | P48735 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 9UO · 6-(6-chloropyridin-2-yl)-N2,N4-bis[(2R)-1,1,1-trifluoropropan-2-yl]-1,3,5-triazine-2,4-diamine · ligand · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.82 | 0.97 | 26 | 9UO |
| 2 | 328 | 0.64 | 0.80 | 37 | empty |
| 3 | 495 | 0.62 | 0.76 | 52 | NA |
| 4 | 247 | 0.58 | 0.79 | 35 | empty |
| 5 | 268 | 0.53 | 0.76 | 35 | NA |
Interfaces
1 interface between chains.
- A–B · 3127 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 6VFZ · Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant… · the same entry in another collection · chain A against A, TM-score 1.00
- P48735 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP], mitochondrial… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P48735
- Elsewhere: RCSB PDB 6VFZ · PDBe 6VFZ · UniProt P48735
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