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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

3id8

2.400 Å

X-ray

2009-07-20

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glucokinase
ID:HXK4_HUMAN
AC:P35557
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.1.2


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:33.728
Number of residues:25
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.387675.000

% Hydrophobic% Polar
55.5044.50
According to VolSite

Ligand :
3id8_1 Structure
HET Code: MRK
Formula: C14H12FN5OS2
Molecular weight: 349.406 g/mol
DrugBank ID: DB08210
Buried Surface Area:68.95 %
Polar Surface area: 139.37 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 2
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-9.890482.8002221.0648


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C11CG1VAL- 623.470Hydrophobic
N4NARG- 633.06158.69H-Bond
(Protein Donor)
N6OARG- 633.32170.47H-Bond
(Ligand Donor)
C9CGPRO- 663.830Hydrophobic
C22CEMET- 2103.740Hydrophobic
S16CD1ILE- 2114.110Hydrophobic
C13CD1ILE- 2113.550Hydrophobic
C12CD1ILE- 2113.470Hydrophobic
F14CD2TYR- 2143.280Hydrophobic
C21CE1TYR- 2143.620Hydrophobic
C22CD1TYR- 2144.10Hydrophobic
N23OHTYR- 2153.38154.18H-Bond
(Ligand Donor)
C21CGGLU- 2213.740Hydrophobic
C22CGGLU- 2214.370Hydrophobic
S16CEMET- 2353.880Hydrophobic
C21CGMET- 2354.350Hydrophobic
C22CGMET- 2353.940Hydrophobic
S1CG1VAL- 4523.970Hydrophobic
S1CG1VAL- 4553.630Hydrophobic