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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:

2r1n

1.700 Å

X-ray

2007-08-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Phosphotriesterase
ID:Q93LD7_RHIRD
AC:Q93LD7
Organism:Rhizobium radiobacter
Reign:Bacteria
TaxID:358
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:14.809
Number of residues:23
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: FE2

Cavity properties

LigandabilityVolume (Å3)
0.473398.250

% Hydrophobic% Polar
48.3151.69
According to VolSite

Ligand :
2r1n_1 Structure
HET Code: EPL
Formula: C11H17O5P
Molecular weight: 260.223 g/mol
DrugBank ID: DB07721
Buried Surface Area:64.41 %
Polar Surface area: 63.8 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 0
Rings: 1
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
26.721219.79841.24406


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
C10CD1ILE- 1064.350Hydrophobic
C11CG2ILE- 1063.80Hydrophobic
O1NE1TRP- 1313.11139.26H-Bond
(Protein Donor)
C10CZ2TRP- 1313.510Hydrophobic
O2NH2ARG- 2542.89124.06H-Bond
(Protein Donor)
C9CZTYR- 2573.770Hydrophobic
C9CD2LEU- 2713.540Hydrophobic
C2CD1LEU- 2713.830Hydrophobic
C11CD2LEU- 3034.30Hydrophobic
C9CZPHE- 3063.480Hydrophobic
C5CBSER- 3084.330Hydrophobic