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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:

3cyz

1.800 Å

X-ray

2008-04-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Pheromone-binding protein ASP1
ID:Q9U9J6_APIME
AC:Q9U9J6
Organism:Apis mellifera
Reign:Eukaryota
TaxID:7460
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:20.032
Number of residues:25
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.830766.125

% Hydrophobic% Polar
71.8128.19
According to VolSite

Ligand :
3cyz_3 Structure
HET Code: 9OD
Formula: C10H15O3
Molecular weight: 183.224 g/mol
DrugBank ID: -
Buried Surface Area:61.08 %
Polar Surface area: 57.2 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 0
Rings: 0
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
27.5997-15.8218-20.4906


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
OE1NZLYS- 173.880Ionic
(Protein Cationic)
OE2NZLYS- 173.770Ionic
(Protein Cationic)
OE1OHTYR- 482.84176.41H-Bond
(Protein Donor)
C7CEMET- 493.380Hydrophobic
C4CD2LEU- 524.120Hydrophobic
C10CD1LEU- 534.490Hydrophobic
C6CD2LEU- 534.440Hydrophobic
C10CG2ILE- 1014.250Hydrophobic
C10CGLEU- 1043.50Hydrophobic
C10CBALA- 1053.380Hydrophobic
C7CBALA- 1053.990Hydrophobic
C4CD1ILE- 1194.420Hydrophobic