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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:

3abx

1.400 Å

X-ray

2009-12-24

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glucanase
ID:B7X9Z2_COPCI
AC:B7X9Z2
Organism:Coprinopsis cinerea
Reign:Eukaryota
TaxID:5346
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:11.196
Number of residues:35
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.7481697.625

% Hydrophobic% Polar
37.5762.43
According to VolSite

Ligand :
3abx_1 Structure
HET Code: RCB
Formula: C24H35NO18
Molecular weight: 625.531 g/mol
DrugBank ID: -
Buried Surface Area:44.67 %
Polar Surface area: 303.5 Å2
Number of
H-Bond Acceptors: 18
H-Bond Donors: 10
Rings: 4
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 10

Mass center Coordinates

XYZ
-9.74959-1.933280.183219


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
C1CCZ3TRP- 614.140Hydrophobic
C2BCBTRP- 614.50Hydrophobic
C2DCH2TRP- 613.170Hydrophobic
C5CCD2TRP- 613.660Hydrophobic
C3CCBSER- 634.160Hydrophobic
C1CCE2TYR- 964.10Hydrophobic
C3DCBPRO- 1494.280Hydrophobic
C3DCBSER- 2363.410Hydrophobic
C6CCDLYS- 32840Hydrophobic
O6CNZLYS- 3282.98171.78H-Bond
(Protein Donor)
O2BOE1GLU- 3322.73172.72H-Bond
(Ligand Donor)
O6COE1GLU- 3322.61167.94H-Bond
(Ligand Donor)
O3DOHOH- 5883.33179.97H-Bond
(Protein Donor)
O2COHOH- 6402.79179.94H-Bond
(Protein Donor)