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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:

1jdt

2.000 Å

X-ray

2001-06-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Purine nucleoside phosphorylase
ID:PNPH_SULSO
AC:P50389
Organism:Sulfolobus solfataricus
Reign:Archaea
TaxID:273057
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B13 %
C87 %


Ligand binding site composition:

B-Factor:30.706
Number of residues:31
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.234651.375

% Hydrophobic% Polar
41.4558.55
According to VolSite

Ligand :
1jdt_3 Structure
HET Code: MTA
Formula: C11H15N5O3S
Molecular weight: 297.333 g/mol
DrugBank ID: DB02282
Buried Surface Area:74.27 %
Polar Surface area: 144.61 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
76.9222122.45715.9711


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
CSCG2VAL- 44.010Hydrophobic
C3'CG2ILE- 644.460Hydrophobic
CSCE1PHE- 1604.30Hydrophobic
C5'CE1PHE- 1603.90Hydrophobic
N1OE1GLU- 1633.04163.51H-Bond
(Protein Donor)
C2'CGMET- 1813.80Hydrophobic
C3'SDMET- 1814.040Hydrophobic
O2'NMET- 1812.99132.02H-Bond
(Protein Donor)
N6OD1ASP- 2053.12149.39H-Bond
(Ligand Donor)