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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:

3pgq

2.800 Å

X-ray

2010-11-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Acetyl-CoA carboxylase
ID:ACAC_YEAST
AC:Q00955
Organism:Saccharomyces cerevisiae
Reign:Eukaryota
TaxID:559292
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B67 %
C33 %


Ligand binding site composition:

B-Factor:77.541
Number of residues:33
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.9751704.375

% Hydrophobic% Polar
55.2544.75
According to VolSite

Ligand :
3pgq_2 Structure
HET Code: GY3
Formula: C18H21N2O3
Molecular weight: 313.371 g/mol
DrugBank ID: -
Buried Surface Area:66.42 %
Polar Surface area: 58.75 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 0
Rings: 3
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
47.5689-35.745919.8153


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
C9CBALA- 16274.490Hydrophobic
C29CBALA- 16273.60Hydrophobic
O12NALA- 16272.93167H-Bond
(Protein Donor)
C10CG2ILE- 16294.40Hydrophobic
C28CBSER- 17084.140Hydrophobic
O12NILE- 17352.98154.35H-Bond
(Protein Donor)
C27CD1ILE- 17354.180Hydrophobic
C28CBILE- 17353.630Hydrophobic
C21CBILE- 17353.510Hydrophobic
C27CD1TYR- 17383.410Hydrophobic
C25CD2LEU- 17564.040Hydrophobic
C26CD1PHE- 19564.170Hydrophobic
O11NGLY- 19982.76169.89H-Bond
(Protein Donor)
C22CBVAL- 20014.140Hydrophobic
C27CG1VAL- 20013.680Hydrophobic
C21CG2VAL- 20013.510Hydrophobic
C29CG2VAL- 20013.620Hydrophobic
C27CG1VAL- 20024.340Hydrophobic
C2CG1VAL- 20244.140Hydrophobic
C10CG1VAL- 20244.390Hydrophobic
C2CD2LEU- 20253.650Hydrophobic