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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:

1f4f

2.000 Å

X-ray

2000-06-07

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
A100 %


Ligand binding site composition:

B-Factor:34.737
Number of residues:40
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 0
Water Molecules: 5
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.998904.500

% Hydrophobic% Polar
42.1657.84
According to VolSite

Ligand :
1f4f_1 Structure
HET Code: TP3
Formula: C17H17N2O9S
Molecular weight: 425.390 g/mol
DrugBank ID: DB04503
Buried Surface Area:48.36 %
Polar Surface area: 195.25 Å2
Number of
H-Bond Acceptors: 9
H-Bond Donors: 1
Rings: 2
Aromatic rings: 1
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 9

Mass center Coordinates

XYZ
15.236714.045334.7083


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
C1CBILE- 794.390Hydrophobic
C2CD1ILE- 794.10Hydrophobic
C17CD1ILE- 794.310Hydrophobic
C16CG2ILE- 794.20Hydrophobic
C5CH2TRP- 803.790Hydrophobic
C1CE2TRP- 803.410Hydrophobic
C5CD1LEU- 1433.80Hydrophobic
C14CGLEU- 1724.110Hydrophobic
C22CZPHE- 1764.010Hydrophobic
C17CBPHE- 1763.920Hydrophobic
O11ND2ASN- 1772.99131.21H-Bond
(Protein Donor)
O26OHOH- 8182.64141.86H-Bond
(Protein Donor)
O27OHOH- 8512.64166.64H-Bond
(Protein Donor)
O29OHOH- 8852.51174.72H-Bond
(Protein Donor)
O11OHOH- 9613.03179.95H-Bond
(Protein Donor)