Research workbench
IDH1 R132H in complex with cpd 1
Analyse IDH1 R132H in complex with cpd 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UMX
- Type
- protein
- Length
- 817 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, VVS
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 412 | 46% helix, 23% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 405 | 45% helix, 22% strand | O75874 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- VVS · 2,6-bis(1H-imidazol-1-ylmethyl)-4-(2,4,4-trimethylpentan-2-yl)phenol · ligand · chains A, B
- GOL · Glycerol · additive · chains 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.85 | 0.86 | 86 | VVS |
| 2 | 557 | 0.74 | 0.81 | 48 | empty |
| 3 | 486 | 0.73 | 0.83 | 50 | NAP |
| 4 | 291 | 0.64 | 0.80 | 38 | empty |
| 5 | 370 | 0.63 | 0.78 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 2930 Ų buried · 54 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 4UMX · PDBe 4UMX · UniProt O75874
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