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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:

1pr4

2.400 Å

X-ray

2003-06-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Purine nucleoside phosphorylase DeoD-type
ID:DEOD_ECO57
AC:P0ABP9
Organism:Escherichia coli O157:H7
Reign:Bacteria
TaxID:83334
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:18.668
Number of residues:28
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.647722.250

% Hydrophobic% Polar
50.0050.00
According to VolSite

Ligand :
1pr4_3 Structure
HET Code: MTP
Formula: C11H14N4O4S
Molecular weight: 298.318 g/mol
DrugBank ID: DB02896
Buried Surface Area:59.86 %
Polar Surface area: 138.82 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
51.129550.768927.7777


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- 644.190Hydrophobic
C5'SDMET- 643.780Hydrophobic
C5'CD2PHE- 1593.790Hydrophobic
S6CE2PHE- 1594.250Hydrophobic
C2'CBGLU- 1794.160Hydrophobic
C2'CGMET- 1803.650Hydrophobic
C3'SDMET- 1803.730Hydrophobic
O2'NMET- 1802.63126.97H-Bond
(Protein Donor)
O3'OE1GLU- 1813.07163.92H-Bond
(Ligand Donor)
O3'OE2GLU- 1812.98129.76H-Bond
(Ligand Donor)
S6CBASP- 2044.350Hydrophobic
CSCG1ILE- 2063.40Hydrophobic