MolNFT v1 · #94669 · protein
Crystal structure of a metabolic reductase with 1-hydroxy-6-(4- hydroxybenzyl)-4-methylpyridin-2(1H)-one
4I3K · Isocitrate dehydrogenase [NADP] cytoplasmic: “Crystal structure of a metabolic reductase with 1-hydroxy-6-(4- hydroxybenzyl)-4-methylpyridin-2(1H)-one”. X-ray diffraction, 3 ligands (NDP, 1BX, SO4), 9 pockets (best druggability…
- PDB
- 4I3K
- Type
- protein
- Length
- 725 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, 1BX, SO4
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 367 | 47% helix, 25% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 358 | 45% helix, 24% strand | O75874 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 1BX · 1-hydroxy-6-(4-hydroxybenzyl)-4-methylpyridin-2(1H)-one · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.63 | 0.80 | 32 | empty |
| 2 | 270 | 0.60 | 0.79 | 28 | empty |
| 3 | 105 | 0.42 | 0.78 | 22 | empty |
| 4 | 69 | 0.40 | 0.80 | 21 | empty |
| 5 | 80 | 0.35 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2100 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 4I3K · Crystal structure of a metabolic reductase with… · 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 0.92
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 4I3K · PDBe 4I3K · UniProt O75874
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