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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:

2qtg

1.840 Å

X-ray

2007-08-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase 1
ID:MTN1_ARATH
AC:Q9T0I8
Organism:Arabidopsis thaliana
Reign:Eukaryota
TaxID:3702
EC Number:3.2.2.9


Chains:

Chain Name:Percentage of Residues
within binding site
A90 %
B10 %


Ligand binding site composition:

B-Factor:17.643
Number of residues:33
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.832405.000

% Hydrophobic% Polar
55.0045.00
According to VolSite

Ligand :
2qtg_1 Structure
HET Code: MTH
Formula: C12H16N4O3S
Molecular weight: 296.345 g/mol
DrugBank ID: DB02933
Buried Surface Area:79.05 %
Polar Surface area: 131.72 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
10.907-0.8159-0.71265


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
CSSDMET- 353.850Hydrophobic
C4'CEMET- 353.90Hydrophobic
CSCG1VAL- 903.970Hydrophobic
S5'CG2VAL- 904.030Hydrophobic
C3'CG1VAL- 903.950Hydrophobic
S5'CG2ILE- 1434.090Hydrophobic
CSCD1ILE- 1454.40Hydrophobic
CSCE1PHE- 1483.690Hydrophobic
C5CD1LEU- 1813.590Hydrophobic
C5'CD1LEU- 1813.890Hydrophobic
N1NZLYS- 1992.78159.38H-Bond
(Protein Donor)
DuArNZLYS- 199493.94Pi/Cation
O2'NMET- 2012.93146.95H-Bond
(Protein Donor)
S5'SDMET- 2013.520Hydrophobic
C3'SDMET- 2013.790Hydrophobic
O2'OE1GLU- 2022.73151.62H-Bond
(Ligand Donor)
O3'OE2GLU- 2022.67152.52H-Bond
(Ligand Donor)
O3'OE1GLU- 2023.1142.41H-Bond
(Ligand Donor)
N6OD1ASP- 2252.94163.15H-Bond
(Ligand Donor)