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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:

3c1y

2.100 Å

X-ray

2008-01-24

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:DNA integrity scanning protein DisA
ID:DISA_THEMA
AC:Q9WY43
Organism:Thermotoga maritima
Reign:Bacteria
TaxID:243274
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A52 %
B48 %


Ligand binding site composition:

B-Factor:26.478
Number of residues:33
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.9851377.000

% Hydrophobic% Polar
35.7864.22
According to VolSite

Ligand :
3c1y_1 Structure
HET Code: 2BA
Formula: C20H22N10O12P2
Molecular weight: 656.396 g/mol
DrugBank ID: -
Buried Surface Area:61.93 %
Polar Surface area: 334.95 Å2
Number of
H-Bond Acceptors: 20
H-Bond Donors: 4
Rings: 7
Aromatic rings: 4
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 2

Mass center Coordinates

XYZ
67.464317.5274-39.7893


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
O2'NGLY- 762.88157.63H-Bond
(Protein Donor)
O2'1NGLY- 762.83166.34H-Bond
(Protein Donor)
N6OLEU- 942.66163.84H-Bond
(Ligand Donor)
N61OLEU- 942.9175.92H-Bond
(Ligand Donor)
N1NLEU- 943159.72H-Bond
(Protein Donor)
N11NLEU- 942.98166.17H-Bond
(Protein Donor)
O1POG1THR- 1072.64165.23H-Bond
(Ligand Donor)
O1P1OG1THR- 1072.52164.46H-Bond
(Protein Donor)
N6OG1THR- 1113.25129.08H-Bond
(Ligand Donor)
N61OG1THR- 1113.14127.87H-Bond
(Ligand Donor)