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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:

4knz

1.300 Å

X-ray

2013-05-10

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
A98 %
B2 %


Ligand binding site composition:

B-Factor:14.007
Number of residues:49
Including
Standard Amino Acids: 41
Non Standard Amino Acids: 1
Water Molecules: 7
Cofactors:
Metals: NA

Cavity properties

LigandabilityVolume (Å3)
0.996914.625

% Hydrophobic% Polar
39.8560.15
According to VolSite

Ligand :
4knz_1 Structure
HET Code: CB3
Formula: C24H21N5O6
Molecular weight: 475.453 g/mol
DrugBank ID: DB03541
Buried Surface Area:64.03 %
Polar Surface area: 180.08 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 10

Mass center Coordinates

XYZ
111.24514.213723.3091


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
C9CD1ILE- 794.470Hydrophobic
CP1CD1ILE- 793.80Hydrophobic
C12CG2ILE- 794.010Hydrophobic
C15CBILE- 793.720Hydrophobic
C9CZ2TRP- 803.480Hydrophobic
C8CD2LEU- 1433.620Hydrophobic
N3OD2ASP- 1692.75162.26H-Bond
(Ligand Donor)
C13CBPHE- 1764.370Hydrophobic
CGCZPHE- 1764.340Hydrophobic
CP1CD2PHE- 1764.030Hydrophobic
CP3CBPHE- 1763.550Hydrophobic
C4ACG2VAL- 2624.290Hydrophobic
C16CG2VAL- 2624.420Hydrophobic
NA2OALA- 2632.98138.18H-Bond
(Ligand Donor)
O1OHOH- 10142.85179.96H-Bond
(Protein Donor)
NA2OHOH- 10233.29122.19H-Bond
(Ligand Donor)
O2OHOH- 10312.68179.97H-Bond
(Protein Donor)
O2OHOH- 10772.93179.96H-Bond
(Protein Donor)