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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:

1kzi

1.750 Å

X-ray

2002-02-06

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:36.180
Number of residues:39
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors: UMP
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.007529.875

% Hydrophobic% Polar
47.7752.23
According to VolSite

Ligand :
1kzi_2 Structure
HET Code: THG
Formula: C19H21N7O6
Molecular weight: 443.413 g/mol
DrugBank ID: DB02031
Buried Surface Area:50.51 %
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
67.269520.2045-6.66731


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
C4'CBILE- 794.090Hydrophobic
C2'CG2ILE- 794.180Hydrophobic
C7CH2TRP- 803.770Hydrophobic
C6CZ2TRP- 804.040Hydrophobic
C9CE2TRP- 804.330Hydrophobic
C9CZ3TRP- 833.850Hydrophobic
C7CD1LEU- 1433.530Hydrophobic
C6'CG2VAL- 2624.040Hydrophobic
N2OALA- 2632.94154.17H-Bond
(Ligand Donor)
C6C5UMP- 3043.360Hydrophobic
OX2OHOH- 4613.37135.14H-Bond
(Protein Donor)
OX2OHOH- 4802.81179.93H-Bond
(Protein Donor)