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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:

3gob

2.050 Å

X-ray

2009-03-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:DdmC
ID:Q5S3I3_STEMA
AC:Q5S3I3
Organism:Stenotrophomonas maltophilia
Reign:Bacteria
TaxID:40324
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:44.024
Number of residues:19
Including
Standard Amino Acids: 19
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.4851171.125

% Hydrophobic% Polar
48.7051.30
According to VolSite

Ligand :
3gob_1 Structure
HET Code: HXX
Formula: C7H3Cl2O3
Molecular weight: 206.003 g/mol
DrugBank ID: -
Buried Surface Area:36.77 %
Polar Surface area: 60.36 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 1
Rings: 1
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
22.1183-9.2272534.1719


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
O1'ND2ASN- 2303.25162.3H-Bond
(Protein Donor)
CL1CD1ILE- 2323.960Hydrophobic
C4CG2ILE- 2323.80Hydrophobic
C2CG1ILE- 2323.810Hydrophobic
O1'NE2HIS- 2513.18163.65H-Bond
(Protein Donor)
CL2CBSER- 2674.440Hydrophobic
CL2CD2LEU- 2824.370Hydrophobic
O1'NE2GLN- 2863.26123.33H-Bond
(Protein Donor)
O2'NE2GLN- 2863.16172.95H-Bond
(Protein Donor)
CL2CGGLN- 2864.420Hydrophobic