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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:

3zdg

2.480 Å

X-ray

2012-11-26

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:7.1007.1007.1000.0007.1002

List of CHEMBLId :

CHEMBL2312568


Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Acetylcholine-binding protein
ID:ACHP_LYMST
AC:P58154
Organism:Lymnaea stagnalis
Reign:Eukaryota
TaxID:6523
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
Q55 %
R45 %


Ligand binding site composition:

B-Factor:19.155
Number of residues:23
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.027489.375

% Hydrophobic% Polar
53.1046.90
According to VolSite

Ligand :
3zdg_13 Structure
HET Code: XRX
Formula: C9H21N2O2
Molecular weight: 189.275 g/mol
DrugBank ID: -
Buried Surface Area:81.57 %
Polar Surface area: 33.98 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 1
Rings: 0
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-56.4718-30.602279.7786


Binding mode :
What is Poseview ?
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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
C11CH2TRP- 533.970Hydrophobic
C11CE2TYR- 893.470Hydrophobic
C2CBMET- 1143.990Hydrophobic
C8SDMET- 1144.090Hydrophobic
N1OTRP- 1432.93134.12H-Bond
(Ligand Donor)
C2CE2TRP- 1433.340Hydrophobic
C8CZ2TRP- 1433.70Hydrophobic
C11CZ3TRP- 1433.950Hydrophobic
C11CD2TYR- 1854.230Hydrophobic
O6OHOH- 20902.94161.31H-Bond
(Protein Donor)