MolNFT v1 · #143483 · protein
IDH1 R132H mutant in complex with IDH305
6B0Z · Isocitrate dehydrogenase [NADP] cytoplasmic: “IDH1 R132H mutant in complex with IDH305”. X-ray diffraction, 2 ligands (C81, NDP), 18 pockets (best druggability 0.89). MolNFT v1 #143483 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6B0Z
- Type
- protein
- Length
- 1,617 residues
- Chains
- 4
- 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
- C81, NDP
- Pockets
- 18 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 399 | 47% helix, 23% strand | O75874 |
| C | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 410 | 46% helix, 22% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 409 | 48% helix, 22% strand | O75874 |
| D | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 399 | 46% helix, 23% strand | O75874 |
Ligands and binding sites
- C81 · (4R)-4-[(1S)-1-fluoroethyl]-3-[2-({(1S)-1-[4-methyl-2'-(trifluoromethyl)[3,4'-bipyridin]-6-yl]ethyl}amino) pyrimidin-4-yl]-1,3-oxazolidin-2-one · ligand · 6 copies · chains A, C, B, D
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, C, B, D
- FLC · Citrate anion · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.89 | 0.90 | 122 | C81 |
| 2 | 886 | 0.88 | 0.89 | 77 | C81 |
| 3 | 172 | 0.67 | 0.87 | 35 | empty |
| 4 | 214 | 0.63 | 0.83 | 32 | empty |
| 5 | 339 | 0.63 | 0.79 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2837 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 2828 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 717 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6B0Z · IDH1 R132H mutant in complex with IDH305 · the same entry in another collection · chain C against C, 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 6B0Z · PDBe 6B0Z · UniProt O75874
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