Research workbench
IDH1 R132H in complex with IDH146
Analyse IDH1 R132H in complex with IDH146 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SUN
- Type
- protein
- Length
- 778 residues
- Chains
- 2
- 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, 70Q, SO4
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 388 | 47% helix, 23% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 390 | 45% helix, 23% strand | O75874 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 70Q · 3-benzyl-N-[3-(dimethylsulfamoyl)phenyl]-4-oxo-3,4-dihydrophthalazine-1-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.67 | 0.76 | 63 | NDP, 70Q, EDO |
| 2 | 596 | 0.66 | 0.76 | 56 | NDP, 70Q |
| 3 | 279 | 0.64 | 0.81 | 34 | empty |
| 4 | 308 | 0.63 | 0.80 | 36 | empty |
| 5 | 585 | 0.62 | 0.74 | 53 | empty |
Interfaces
1 interface between chains.
- A–B · 2101 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
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 5SUN · PDBe 5SUN · UniProt O75874
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