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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:

4a39

1.600 Å

X-ray

2011-09-30

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized protein
ID:Q9I012_PSEAE
AC:Q9I012
Organism:Pseudomonas aeruginosa
Reign:Bacteria
TaxID:208964
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:7.530
Number of residues:29
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 1
Water Molecules: 4
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.253354.375

% Hydrophobic% Polar
45.7154.29
According to VolSite

Ligand :
4a39_1 Structure
HET Code: GEM
Formula: C7H12N3O4S
Molecular weight: 234.253 g/mol
DrugBank ID: DB04489
Buried Surface Area:59.89 %
Polar Surface area: 169.2 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 3
Rings: 0
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-1.67047-7.590738.42913


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
O15CZARG- 2183.550Ionic
(Protein Cationic)
O13CZARG- 2183.840Ionic
(Protein Cationic)
O15NH2ARG- 2182.66174.03H-Bond
(Protein Donor)
O13NH1ARG- 2182.99140.75H-Bond
(Protein Donor)
O14ND2ASN- 2272.77174.05H-Bond
(Protein Donor)
O14NH1ARG- 2283.01174.92H-Bond
(Protein Donor)
O15NH2ARG- 2283165.35H-Bond
(Protein Donor)
O14CZARG- 2283.90Ionic
(Protein Cationic)
O15CZARG- 2283.750Ionic
(Protein Cationic)
C5CBALA- 2714.360Hydrophobic
C5CE2TYR- 3063.30Hydrophobic
C10CZTYR- 30640Hydrophobic
C6CD2LEU- 3184.080Hydrophobic
S7CG2THR- 3333.290Hydrophobic
C6CBTHR- 3333.450Hydrophobic
C5CG2THR- 33340Hydrophobic
O12ZN ZN- 13762.730Metal Acceptor
O13ZN ZN- 13762.220Metal Acceptor