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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:

4l5a

2.300 Å

X-ray

2013-06-10

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:S-methyl-5'-thioadenosine phosphorylase
ID:I0B503_SCHMA
AC:I0B503
Organism:Schistosoma mansoni
Reign:Eukaryota
TaxID:6183
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
D93 %
F7 %


Ligand binding site composition:

B-Factor:31.564
Number of residues:31
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.840735.750

% Hydrophobic% Polar
40.3759.63
According to VolSite

Ligand :
4l5a_4 Structure
HET Code: TBN
Formula: C11H14N4O4
Molecular weight: 266.253 g/mol
DrugBank ID: DB03172
Buried Surface Area:76 %
Polar Surface area: 126.65 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
67.589229.592553.2384


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
C3'CGPRO- 634.10Hydrophobic
C1'CBALA- 883.80Hydrophobic
C5'CE1PHE- 1873.790Hydrophobic
C2'CGMET- 2063.70Hydrophobic
C3'SDMET- 2063.920Hydrophobic
O2'NMET- 2062.94143.59H-Bond
(Protein Donor)
N6OD1ASP- 2303.38166.97H-Bond
(Ligand Donor)
N6OD1ASP- 2323.15168.6H-Bond
(Ligand Donor)
O3'OHOH- 4033.18179.98H-Bond
(Protein Donor)
N1OHOH- 4093163.79H-Bond
(Protein Donor)