Research workbench
IDH1 R132H mutant in complex with IDH889
Analyse IDH1 R132H mutant in complex with IDH889 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TQH
- Type
- protein
- Length
- 1,618 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
- 7J2, NDP
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 401 | 46% helix, 23% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 407 | 48% helix, 22% strand | O75874 |
| C | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 408 | 45% helix, 22% strand | O75874 |
| D | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 402 | 47% helix, 23% strand | O75874 |
Ligands and binding sites
- 7J2 · (4S)-3-[2-({(1S)-1-[5-(4-fluoro-3-methylphenyl) pyrimidin-2-yl]ethyl}amino)pyrimidin-4-yl]-4-(propan-2-yl)-1,3-oxazolidin-2-one · ligand · 4 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, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.89 | 0.90 | 105 | 7J2 |
| 2 | 584 | 0.87 | 0.92 | 64 | 7J2 |
| 3 | 315 | 0.78 | 0.89 | 43 | empty |
| 4 | 362 | 0.63 | 0.79 | 38 | empty |
| 5 | 317 | 0.62 | 0.79 | 39 | NDP |
Interfaces
3 interfaces between chains.
- A–C · 2964 Ų buried · 42 hydrogen bonds · protein-protein
- B–D · 2930 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 755 Ų buried · 10 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 5TQH · PDBe 5TQH · UniProt O75874
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