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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:

4da6

1.700 Å

X-ray

2012-01-12

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Purine nucleoside phosphorylase DeoD-type
ID:DEOD_BACSU
AC:O34925
Organism:Bacillus subtilis
Reign:Bacteria
TaxID:224308
EC Number:2.4.2.1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:24.096
Number of residues:29
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 2
Water Molecules: 2
Cofactors:
Metals: CL CL

Cavity properties

LigandabilityVolume (Å3)
0.887641.250

% Hydrophobic% Polar
52.6347.37
According to VolSite

Ligand :
4da6_1 Structure
HET Code: GA2
Formula: C9H13N5O4
Molecular weight: 255.231 g/mol
DrugBank ID: DB01004
Buried Surface Area:61.78 %
Polar Surface area: 134.99 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 4
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-50.653121.034623.9543


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
C4'CGMET- 644.430Hydrophobic
C3'SDMET- 643.540Hydrophobic
C3'CD1PHE- 1594.480Hydrophobic
C1'CBGLU- 1784.080Hydrophobic
C4'CGMET- 1793.510Hydrophobic
C2'SDMET- 1793.860Hydrophobic
O4'OE1GLU- 1803.37125.04H-Bond
(Ligand Donor)
O4'OE2GLU- 1802.71163.61H-Bond
(Ligand Donor)
N7OGSER- 2022.75168.45H-Bond
(Protein Donor)