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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:

4dae

2.350 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:31.605
Number of residues:30
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: CL

Cavity properties

LigandabilityVolume (Å3)
0.392391.500

% Hydrophobic% Polar
45.6954.31
According to VolSite

Ligand :
4dae_1 Structure
HET Code: 6CR
Formula: C10H12ClN5O4
Molecular weight: 301.686 g/mol
DrugBank ID: -
Buried Surface Area:64.17 %
Polar Surface area: 139.54 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-50.333620.754923.1669


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
C3'CGMET- 644.360Hydrophobic
C5'SDMET- 643.820Hydrophobic
C5'CD1PHE- 1593.720Hydrophobic
C2'CBGLU- 1784.120Hydrophobic
C2'CGMET- 1793.870Hydrophobic
C5'SDMET- 1793.740Hydrophobic
O2'NMET- 1792.97129.51H-Bond
(Protein Donor)
O2'OE2GLU- 1803.44129.5H-Bond
(Ligand Donor)
O3'OE2GLU- 1802.51169.59H-Bond
(Ligand Donor)
N7OGSER- 2022.8174.41H-Bond
(Protein Donor)
CL1CG2VAL- 2053.630Hydrophobic