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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:

3jq6

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:18.325
Number of residues:25
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: NAP
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.911725.625

% Hydrophobic% Polar
52.5647.44
According to VolSite

Ligand :
3jq6_2 Structure
HET Code: DX1
Formula: C12H18N6
Molecular weight: 246.312 g/mol
DrugBank ID: -
Buried Surface Area:67.86 %
Polar Surface area: 103.6 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
8.0340618.640261.0664


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
N11OGSER- 953.43161.19H-Bond
(Ligand Donor)
C14CZPHE- 974.060Hydrophobic
DuArDuArPHE- 973.950Aromatic Face/Face
DuArDuArPHE- 973.640Aromatic Face/Face
N12OHTYR- 1742.59166.66H-Bond
(Ligand Donor)
C15CG2VAL- 20640Hydrophobic
C17CD2LEU- 2093.750Hydrophobic
C18CGPRO- 2104.170Hydrophobic
C18CEMET- 2134.160Hydrophobic
C14CZ2TRP- 2214.030Hydrophobic
N11O2DNAP- 2693.34121.04H-Bond
(Ligand Donor)
N11O2ANAP- 2693.08163.28H-Bond
(Ligand Donor)
C15C4NNAP- 2694.440Hydrophobic