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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:

3gb4

2.050 Å

X-ray

2009-02-18

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
B100 %


Ligand binding site composition:

B-Factor:43.733
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.492506.250

% Hydrophobic% Polar
61.3338.67
According to VolSite

Ligand :
3gb4_2 Structure
HET Code: D3M
Formula: C8H5Cl2O3
Molecular weight: 220.030 g/mol
DrugBank ID: -
Buried Surface Area:60.28 %
Polar Surface area: 49.36 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 0
Rings: 1
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-55.2114-50.92825.60754


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
C8CD2LEU- 1554.460Hydrophobic
CL1CD1LEU- 1583.650Hydrophobic
C8CD1LEU- 1584.170Hydrophobic
C3CD2LEU- 2023.650Hydrophobic
C3CEMET- 2034.320Hydrophobic
CL2CZPHE- 2063.990Hydrophobic
O2ND2ASN- 2302.9172.63H-Bond
(Protein Donor)
C6CD1ILE- 2324.130Hydrophobic
C2CG1ILE- 2323.970Hydrophobic
C5CD1ILE- 2323.770Hydrophobic
O2NE2HIS- 2512.95170.88H-Bond
(Protein Donor)
CL2CD2LEU- 2823.850Hydrophobic
CL2CE2TRP- 2854.160Hydrophobic
C8CZ2TRP- 2854.30Hydrophobic
O1NE1TRP- 2852.95160.15H-Bond
(Protein Donor)
C8CD1LEU- 2904.110Hydrophobic