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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:

3jq7

1.800 Å

X-ray

2009-09-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Pteridine reductase, putative
ID:Q581W1_TRYB2
AC:Q581W1
Organism:Trypanosoma brucei brucei
Reign:Eukaryota
TaxID:185431
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:26.754
Number of residues:22
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors: NAP
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.795884.250

% Hydrophobic% Polar
45.0454.96
According to VolSite

Ligand :
3jq7_2 Structure
HET Code: DX2
Formula: C12H11N7
Molecular weight: 253.263 g/mol
DrugBank ID: DB00384
Buried Surface Area:74.55 %
Polar Surface area: 129.62 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 3
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
-17.565717.15153.75747


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
N2OGSER- 952.72155.51H-Bond
(Ligand Donor)
DuArDuArPHE- 973.790Aromatic Face/Face
DuArDuArPHE- 973.860Aromatic Face/Face
N4OHTYR- 1742.75162.16H-Bond
(Ligand Donor)
CAFCG2VAL- 2064.230Hydrophobic
CAGCD2LEU- 2093.510Hydrophobic
CAECGLEU- 2094.010Hydrophobic
CADCD2LEU- 2093.240Hydrophobic
CAGCGPRO- 2103.960Hydrophobic
CAECEMET- 2134.260Hydrophobic
N1O2ANAP- 2692.75157.45H-Bond
(Ligand Donor)
N2O2ANAP- 2693.16134.85H-Bond
(Ligand Donor)
N3O2DNAP- 2692.71156.98H-Bond
(Protein Donor)