MolNFT v1 · #67525 · protein
Crystal structure of human glucokinase in complex with a synthetic activator
3IMX: “Crystal structure of human glucokinase in complex with a synthetic activator”. X-ray diffraction, 3 ligands (B84, GLC, NA), 3 pockets (best druggability 0.67). MolNFT v1 #67525 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3IMX
- Type
- protein
- Length
- 447 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucokinase
- UniProt
- Q53Y25
- Ligands
- B84, GLC, NA
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucokinase | protein | 447 | 43% helix, 21% strand | Q53Y25 |
Ligands and binding sites
- B84 · (2R)-3-cyclopentyl-N-(5-methoxy[1,3]thiazolo[5,4-b]pyridin-2-yl)-2-{4-[(4-methylpiperazin-1-yl)sulfonyl]phenyl}propanamide · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.67 | 0.82 | 32 | B84 |
| 2 | 324 | 0.64 | 0.80 | 41 | GLC |
| 3 | 144 | 0.42 | 0.75 | 26 | empty |
Compared structures
- 3IMX · Crystal Structure of human glucokinase in complex with a synthetic activator · 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 Q53Y25
- Elsewhere: RCSB PDB 3IMX · PDBe 3IMX · UniProt Q53Y25
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