Research workbench
Crystal structure of human IDH1 in complex with GSK321A
Analyse Crystal structure of human IDH1 in complex with GSK321A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DE1
- Type
- protein
- Length
- 799 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
- NAP, 59D
- Pockets
- 10 · best druggability 0.82
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 | 399 | 46% helix, 23% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 400 | 46% helix, 23% strand | O75874 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 59D · (7R)-1-(4-fluorobenzyl)-N-{3-[(1S)-1-hydroxyethyl]phenyl}-7-methyl-5-(1H-pyrrol-2-ylcarbonyl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridine-3-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.82 | 0.83 | 93 | 59D, NAP |
| 2 | 381 | 0.61 | 0.77 | 33 | empty |
| 3 | 265 | 0.59 | 0.79 | 37 | empty |
| 4 | 222 | 0.56 | 0.78 | 35 | empty |
| 5 | 55 | 0.42 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2349 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 5DE1 · Crystal structure of human IDH1 in complex with GSK321A · 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 A against A, TM-score 0.93
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 5DE1 · PDBe 5DE1 · UniProt O75874
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