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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:

3ppr

2.100 Å

X-ray

2010-11-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glycine betaine/carnitine/choline-binding protein OpuCC
ID:OPUCC_BACSU
AC:O32243
Organism:Bacillus subtilis
Reign:Bacteria
TaxID:224308
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:25.430
Number of residues:20
Including
Standard Amino Acids: 20
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.324411.750

% Hydrophobic% Polar
36.8963.11
According to VolSite

Ligand :
3ppr_2 Structure
HET Code: 4CS
Formula: C6H10N2O2
Molecular weight: 142.156 g/mol
DrugBank ID: -
Buried Surface Area:75.76 %
Polar Surface area: 66.13 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 2
Rings: 1
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
15.908638.786228.9428


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
OXTNE2GLN- 392.82165.21H-Bond
(Protein Donor)
CBSDMET- 4140Hydrophobic
CBCD2TYR- 913.390Hydrophobic
CADCBASN- 1354.280Hydrophobic
NAGOASN- 1352.82126.06H-Bond
(Ligand Donor)
CAACD2TYR- 1373.720Hydrophobic
CAACE1TYR- 2174.320Hydrophobic
CAACGTYR- 2413.970Hydrophobic