MolNFT v1 · #142725 · protein
Crystal structures of IDH1 R132H in complex with ag-881
6ADG · Isocitrate dehydrogenase [NADP] cytoplasmic: “Crystal structures of IDH1 R132H in complex with ag-881”. X-ray diffraction, 3 ligands (NDP, 9UO, MG), 20 pockets (best druggability 0.83). MolNFT v1 #142725 on GenesisL1: 3D structure…
- PDB
- 6ADG
- Type
- protein
- Length
- 1,213 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
- NDP, 9UO, MG
- Pockets
- 20 · best druggability 0.83
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 | 412 | 48% helix, 22% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 411 | 48% helix, 22% strand | O75874 |
| C | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 390 | 47% helix, 22% strand | O75874 |
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 · 2 copies · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.83 | 0.97 | 32 | 9UO |
| 2 | 165 | 0.73 | 0.90 | 40 | empty |
| 3 | 116 | 0.64 | 0.88 | 30 | empty |
| 4 | 518 | 0.62 | 0.75 | 60 | NDP |
| 5 | 233 | 0.59 | 0.80 | 31 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3085 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 212 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ADG · Crystal Structures of IDH1 R132H in complex with AG-881 · 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 6ADG · PDBe 6ADG · UniProt O75874
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.