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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:

3isi

2.200 Å

X-ray

2009-08-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Putative dipeptidase
ID:Q93J45_STRCO
AC:Q93J45
Organism:Streptomyces coelicolor / M145)
Reign:Bacteria
TaxID:100226
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
X100 %


Ligand binding site composition:

B-Factor:23.350
Number of residues:25
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 2
Water Molecules: 2
Cofactors:
Metals: ZN ZN

Cavity properties

LigandabilityVolume (Å3)
0.8031042.875

% Hydrophobic% Polar
32.0467.96
According to VolSite

Ligand :
3isi_1 Structure
HET Code: B88
Formula: C7H12NO6P
Molecular weight: 237.147 g/mol
DrugBank ID: -
Buried Surface Area:66.99 %
Polar Surface area: 157.84 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 1
Rings: 0
Aromatic rings: 0
Anionic atoms: 3
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-12.981438.4923-4.17053


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
C12CE1TYR- 684.260Hydrophobic
O4NE2HIS- 1502.99126.56H-Bond
(Protein Donor)
O5NE2HIS- 1502.82153.97H-Bond
(Protein Donor)
O1NH1ARG- 2233.19161.45H-Bond
(Protein Donor)
O6NEARG- 2233.1166.91H-Bond
(Protein Donor)
O6CZARG- 2233.780Ionic
(Protein Cationic)
O3NZLYS- 2473.02140.65H-Bond
(Protein Donor)
O3NZLYS- 2473.020Ionic
(Protein Cationic)
C13CZPHE- 2483.740Hydrophobic
O5ZN ZN- 30012.20Metal Acceptor
O1ZN ZN- 30012.380Metal Acceptor