Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

2bfm

2.600 Å

X-ray

2004-12-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Pteridine reductase 1
ID:PTR1_LEIMA
AC:Q01782
Organism:Leishmania major
Reign:Eukaryota
TaxID:5664
EC Number:1.5.1.33


Chains:

Chain Name:Percentage of Residues
within binding site
B92 %
C8 %


Ligand binding site composition:

B-Factor:31.163
Number of residues:24
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors: NDP
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.863502.875

% Hydrophobic% Polar
63.0936.91
According to VolSite

Ligand :
2bfm_2 Structure
HET Code: TOP
Formula: C14H18N4O3
Molecular weight: 290.318 g/mol
DrugBank ID: DB00440
Buried Surface Area:54.02 %
Polar Surface area: 105.51 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
30.140734.161571.6821


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
C14CE2PHE- 1133.590Hydrophobic
DuArDuArPHE- 1133.660Aromatic Face/Face
C20CD1LEU- 1883.450Hydrophobic
C21CD2LEU- 1883.960Hydrophobic
C18CD2LEU- 1883.890Hydrophobic
C14CZTYR- 1914.290Hydrophobic
N4OHTYR- 1943.11151.72H-Bond
(Ligand Donor)
C9CD2LEU- 2263.440Hydrophobic
C10CD1LEU- 2293.940Hydrophobic
C17CEMET- 2334.040Hydrophobic