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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:

3gsi

2.000 Å

X-ray

2009-03-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Dimethylglycine oxidase
ID:DMGO_ARTGO
AC:Q9AGP8
Organism:Arthrobacter globiformis
Reign:Bacteria
TaxID:1665
EC Number:1.5.3.10


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:18.649
Number of residues:40
Including
Standard Amino Acids: 37
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.7201778.625

% Hydrophobic% Polar
43.2656.74
According to VolSite

Ligand :
3gsi_1 Structure
HET Code: THG
Formula: C19H21N7O6
Molecular weight: 443.413 g/mol
DrugBank ID: DB02031
Buried Surface Area:57.27 %
Polar Surface area: 212.92 Å2
Number of
H-Bond Acceptors: 11
H-Bond Donors: 6
Rings: 3
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 9

Mass center Coordinates

XYZ
51.158385.559742.1084


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
C7CD1LEU- 5083.970Hydrophobic
C9CE1TYR- 5394.070Hydrophobic
CGCBTYR- 5394.410Hydrophobic
C3'CE1TYR- 5393.380Hydrophobic
N1OG1THR- 5542.58170.97H-Bond
(Protein Donor)
N2OG1THR- 5543.1120.54H-Bond
(Ligand Donor)
C5'CG2THR- 5544.060Hydrophobic
N8OGLY- 5662.88124.8H-Bond
(Ligand Donor)
CBCE2TYR- 6314.350Hydrophobic
CBCZPHE- 6323.840Hydrophobic
C6'CD1LEU- 6493.990Hydrophobic
N3OE1GLU- 6583.48121.6H-Bond
(Ligand Donor)
N3OE2GLU- 6582.54170.87H-Bond
(Ligand Donor)
N2OE1GLU- 6582.64157.45H-Bond
(Ligand Donor)
C2'CBTYR- 6993.970Hydrophobic
CGCE1PHE- 7194.060Hydrophobic
O11OHOH- 10462.78179.96H-Bond
(Protein Donor)
O4OHOH- 12192.75179.97H-Bond
(Protein Donor)