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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:

2z0x

1.640 Å

X-ray

2007-05-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized protein
ID:Q5SHN1_THET8
AC:Q5SHN1
Organism:Thermus thermophilus
Reign:Bacteria
TaxID:300852
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:9.781
Number of residues:36
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.306448.875

% Hydrophobic% Polar
45.8654.14
According to VolSite

Ligand :
2z0x_1 Structure
HET Code: 5CA
Formula: C13H19N7O7S2
Molecular weight: 449.463 g/mol
DrugBank ID: DB02684
Buried Surface Area:50.58 %
Polar Surface area: 268.66 Å2
Number of
H-Bond Acceptors: 12
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
19.842541.461235.2841


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
NOTHR- 312.69151.59H-Bond
(Ligand Donor)
CBCBALA- 374.10Hydrophobic
SGCG2ILE- 483.570Hydrophobic
O1SNSER- 513.31121.09H-Bond
(Protein Donor)
C4'CD2LEU- 523.70Hydrophobic
C1'CD2LEU- 524.350Hydrophobic
C1'CD1ILE- 1004.40Hydrophobic
NOGLY- 1012.78155.22H-Bond
(Ligand Donor)
SGCBALA- 1293.870Hydrophobic
SGCD2LEU- 1363.880Hydrophobic
O1SOHOH- 2182.58121.24H-Bond
(Protein Donor)