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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:

1aob

2.100 Å

X-ray

1997-06-30

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:22.292
Number of residues:21
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.6511090.125

% Hydrophobic% Polar
30.3469.66
According to VolSite

Ligand :
1aob_1 Structure
HET Code: DDU
Formula: C9H12N2O4
Molecular weight: 212.203 g/mol
DrugBank ID: DB03274
Buried Surface Area:51.26 %
Polar Surface area: 78.87 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 2
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
-28.4613-9.3517320.4585


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
C2'SGCYS- 1464.160Hydrophobic
C2'CBSER- 16740Hydrophobic
O2NASP- 1692.91161.47H-Bond
(Protein Donor)
C1'CBASP- 16940Hydrophobic
N3OD1ASN- 1773175.75H-Bond
(Ligand Donor)
O4ND2ASN- 1772.65125.11H-Bond
(Protein Donor)