Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

1ysz

2.650 Å

X-ray

2005-02-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Endoplasmin
ID:ENPL_CANLF
AC:P41148
Organism:Canis lupus familiaris
Reign:Eukaryota
TaxID:9615
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:43.648
Number of residues:34
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.919550.125

% Hydrophobic% Polar
42.9457.06
According to VolSite

Ligand :
1ysz_1 Structure
HET Code: NEC
Formula: C12H16N6O4
Molecular weight: 308.293 g/mol
DrugBank ID: DB03719
Buried Surface Area:51.22 %
Polar Surface area: 148.41 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
44.790232.039739.1578


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
N6OD2ASP- 1492.89169.8H-Bond
(Ligand Donor)
C1'SDMET- 1543.830Hydrophobic
N5'OASN- 1623.05159.66H-Bond
(Ligand Donor)
C4'CBASN- 1624.410Hydrophobic
C1'CBASN- 1624.110Hydrophobic
C4'CD2LEU- 1634.310Hydrophobic
C1'CD2LEU- 1634.190Hydrophobic
C52CG1VAL- 1973.950Hydrophobic
C52CE2TYR- 2003.410Hydrophobic
O5'OHOH- 3512.53179.97H-Bond
(Protein Donor)