MolNFT v1 · #110284 · protein
Crystal structure of a metabolic reductase with (E)-5-((1-methyl-5- oxo-2-thioxoimidazolidin-4-YLIDENE)METHYL)PYRIDIN-2(1H)-one
4XRX · Isocitrate dehydrogenase [NADP] cytoplasmic: “Crystal structure of a metabolic reductase with (E)-5-((1-methyl-5…”. X-ray diffraction, 2 ligands (NDP, 42V), 9 pockets (best druggability 0.66). MolNFT v1 #110284 on GenesisL1: 3D…
- PDB
- 4XRX
- Type
- protein
- Length
- 776 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, 42V
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 2 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 | 390 | 45% helix, 23% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 386 | 47% helix, 22% strand | O75874 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 42V · 5-[(E)-(1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl]pyridin-2(1H)-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.66 | 0.77 | 60 | NDP |
| 2 | 486 | 0.64 | 0.76 | 44 | empty |
| 3 | 271 | 0.62 | 0.80 | 37 | empty |
| 4 | 367 | 0.61 | 0.77 | 38 | empty |
| 5 | 280 | 0.58 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2156 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 4XRX · 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 0.93
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 4XRX · PDBe 4XRX · UniProt O75874
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