MolNFT v1 · #147039 · protein
Crystal structure of glucokinase in complex with compound 72
6E0I: “Crystal structure of glucokinase in complex with compound 72”. X-ray diffraction, 2 ligands (HKG, GLC), 4 pockets (best druggability 0.56). MolNFT v1 #147039 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6E0I
- Type
- protein
- Length
- 448 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucokinase
- EC
- 2.7.1.2
- UniProt
- P35557
- Ligands
- HKG, GLC
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucokinase (EC 2.7.1.2) | protein | 448 | 46% helix, 20% strand | P35557 |
Ligands and binding sites
- HKG · 1-{4-[5-({3-[(2-methylpyridin-3-yl)oxy]-5-[(pyridin-2-yl)sulfanyl]pyridin-2-yl}amino)-1,2,4-thiadiazol-3-yl]piperidin-1 -yl}ethan-1-one · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.56 | 0.80 | 32 | DMS |
| 2 | 290 | 0.54 | 0.75 | 37 | empty |
| 3 | 198 | 0.53 | 0.77 | 21 | HKG |
| 4 | 69 | 0.37 | 0.77 | 17 | empty |
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 P35557
- Elsewhere: RCSB PDB 6E0I · PDBe 6E0I · UniProt P35557
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