MolNFT v1 · #150120 · protein
Inhibited structure of impdh from pseudomonas aeruginosa
6GK9 · Inosine-5'-monophosphate dehydrogenase: “Inhibited structure of impdh from pseudomonas aeruginosa”. X-ray diffraction, 2 ligands (F2K, SO4), 20 pockets (best druggability 0.80). MolNFT v1 #150120 on GenesisL1: 3D structure, binding…
- PDB
- 6GK9
- Type
- protein
- Length
- 3,142 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-5'-monophosphate dehydrogenase
- EC
- 1.1.1.205
- UniProt
- Q9HXM5
- Ligands
- F2K, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 8 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 424 | 36% helix, 23% strand | Q9HXM5 |
| B | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 424 | 35% helix, 23% strand | Q9HXM5 |
| C | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 381 | 36% helix, 20% strand | Q9HXM5 |
| D | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 424 | 36% helix, 24% strand | Q9HXM5 |
| E | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 424 | 35% helix, 24% strand | Q9HXM5 |
| F | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 317 | 37% helix, 22% strand | Q9HXM5 |
| G | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 329 | 35% helix, 20% strand | Q9HXM5 |
| H | Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) | protein | 419 | 36% helix, 22% strand | Q9HXM5 |
Ligands and binding sites
- F2K · (5~{S})-7-azanyl-5-(4-chlorophenyl)-2,4-bis(oxidanylidene)-1,5-dihydropyrano[2,3-d]pyrimidine-6-carbonitrile · ligand · 2 copies · chains A, B, D, H
- SO4 · Sulfate ion · ion · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.80 | 0.82 | 75 | F2K |
| 2 | 984 | 0.78 | 0.80 | 70 | F2K |
| 3 | 1195 | 0.71 | 0.75 | 67 | empty |
| 4 | 448 | 0.63 | 0.77 | 66 | empty |
| 5 | 549 | 0.63 | 0.75 | 70 | empty |
Interfaces
12 interfaces between chains.
- A–F · 1549 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1520 Ų buried · 14 hydrogen bonds · protein-protein
- D–H · 1509 Ų buried · 17 hydrogen bonds · protein-protein
- E–H · 1496 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1439 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6GK9 · Inhibited structure of IMPDH from Pseudomonas aeruginosa · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9HXM5
- Elsewhere: RCSB PDB 6GK9 · PDBe 6GK9 · UniProt Q9HXM5
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