MolNFT v1 · #185202 · protein
Crystal structure of ivosidenib-resistant IDH1 variant R132C S280F in complex with NADPH and CA2+/2-oxoglutarate
7PJM · Isocitrate dehydrogenase [NADP] cytoplasmic: “Crystal structure of ivosidenib-resistant IDH1 variant R132C S280F in complex with NADPH and…”. X-ray diffraction, 4 ligands (AKG, NDP, CA), 10 pockets (best druggability 0.78). MolNFT…
- PDB
- 7PJM
- Type
- protein
- Length
- 1,240 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
- AKG, NDP, CA, CL
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 415 | 47% helix, 22% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 411 | 47% helix, 23% strand | O75874 |
| C | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 414 | 48% helix, 21% strand | O75874 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 3 copies · chains A, B, C
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.78 | 0.81 | 73 | AKG, NDP, CA |
| 2 | 876 | 0.77 | 0.80 | 73 | CA, AKG, NDP |
| 3 | 800 | 0.72 | 0.77 | 76 | empty |
| 4 | 184 | 0.48 | 0.76 | 26 | empty |
| 5 | 161 | 0.45 | 0.76 | 30 | CA, AKG, NDP |
Interfaces
3 interfaces between chains.
- A–B · 3657 Ų buried · 60 hydrogen bonds · protein-protein
- A–C · 322 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 122 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7PJM · Crystal Structure of Ivosidenib-resistant IDH1 variant R132C S280F in complex with NADPH… · the same entry in another collection · chain A against A, TM-score 1.00
- O75874 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] cytoplasmic (O75874) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 7PJM · PDBe 7PJM · UniProt O75874
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