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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:

1tsd

1.950 Å

X-ray

1995-08-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Thymidylate synthase
ID:TYSY_ECOLI
AC:P0A884
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A3 %
B97 %


Ligand binding site composition:

B-Factor:35.817
Number of residues:32
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: UMP
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.298715.500

% Hydrophobic% Polar
56.6043.40
According to VolSite

Ligand :
1tsd_2 Structure
HET Code: F89
Formula: C27H22N4O6
Molecular weight: 498.487 g/mol
DrugBank ID: -
Buried Surface Area:60.38 %
Polar Surface area: 154.06 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 2
Rings: 5
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 8

Mass center Coordinates

XYZ
46.939240.57221.0216


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
C17CBSER- 543.660Hydrophobic
N12OE1GLU- 583.36152.96H-Bond
(Ligand Donor)
C17CG1VAL- 774.020Hydrophobic
C8CG2ILE- 793.780Hydrophobic
C15CBILE- 793.730Hydrophobic
CGCBILE- 793.670Hydrophobic
C16CG2ILE- 793.840Hydrophobic
C6ACG1ILE- 793.60Hydrophobic
C13CG2ILE- 793.930Hydrophobic
C7CZ2TRP- 803.430Hydrophobic
C6CD2LEU- 1434.070Hydrophobic
N2OD2ASP- 1692.83172.32H-Bond
(Ligand Donor)
C11CBPHE- 1763.920Hydrophobic
C13CBPHE- 1763.910Hydrophobic
DuArDuArPHE- 1763.470Aromatic Face/Face
C3MCE1TYR- 2093.810Hydrophobic
C3MCG1VAL- 2623.930Hydrophobic
C3MCBALA- 2634.260Hydrophobic
C3MC4'UMP- 2653.970Hydrophobic
C1AC1'UMP- 2654.240Hydrophobic