MolNFT v1 · #151871 · protein
Structure of human imp dehydrogenase, isoform 2, bound to GDP
6I0M · Inosine-5'-monophosphate dehydrogenase 2: “Structure of human imp dehydrogenase, isoform 2, bound to GDP”. X-ray diffraction, 3 ligands (GDP, 5GP, SO4), 10 pockets (best druggability 0.75). MolNFT v1 #151871 on GenesisL1: 3D…
- PDB
- 6I0M
- Type
- protein
- Length
- 894 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-5'-monophosphate dehydrogenase 2
- EC
- 1.1.1.205
- UniProt
- P12268
- Ligands
- GDP, 5GP, SO4
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) | protein | 450 | 36% helix, 18% strand | P12268 |
| B | Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) | protein | 444 | 36% helix, 18% strand | P12268 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains A, B
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.75 | 0.78 | 90 | GDP |
| 2 | 349 | 0.62 | 0.78 | 33 | 5GP, SO4 |
| 3 | 197 | 0.48 | 0.76 | 25 | 5GP |
| 4 | 96 | 0.43 | 0.79 | 22 | empty |
| 5 | 56 | 0.42 | 0.82 | 16 | GDP |
Interfaces
1 interface between chains.
- A–B · 1334 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6I0M · Structure of human IMP dehydrogenase, isoform 2, bound to GDP · the same entry in another collection · chain A against A, TM-score 1.00
- P12268 · AlphaFold monomer V2.0 prediction for inosine-5'-monophosphate dehydrogenase 2 (P12268) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P12268
- Elsewhere: RCSB PDB 6I0M · PDBe 6I0M · UniProt P12268
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