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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:

1h5t

1.900 Å

X-ray

2001-05-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glucose-1-phosphate thymidylyltransferase 1
ID:RMLA1_ECOLI
AC:P37744
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A79 %
D21 %


Ligand binding site composition:

B-Factor:24.175
Number of residues:26
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.426421.875

% Hydrophobic% Polar
56.0044.00
According to VolSite

Ligand :
1h5t_1 Structure
HET Code: TYD
Formula: C10H13N2O11P2
Molecular weight: 399.165 g/mol
DrugBank ID: DB03103
Buried Surface Area:61.78 %
Polar Surface area: 220.27 Å2
Number of
H-Bond Acceptors: 11
H-Bond Donors: 2
Rings: 2
Aromatic rings: 0
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
37.28142.9045237.9274


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'CD1LEU- 463.670Hydrophobic
C4'CD1TYR- 1154.250Hydrophobic
O3'NGLY- 1162.76162.04H-Bond
(Protein Donor)
C3'CBLEU- 1193.870Hydrophobic
C2'CD2LEU- 1194.460Hydrophobic
C2'CGPRO- 1204.430Hydrophobic
O1BNARG- 2202.93168.02H-Bond
(Protein Donor)
C5MCDARG- 2204.220Hydrophobic
O2NSER- 2522.72177.44H-Bond
(Protein Donor)
N3OHOH- 21252.89146.28H-Bond
(Ligand Donor)