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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:

1qy5

1.750 Å

X-ray

2003-09-09

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:24.986
Number of residues:36
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.201529.875

% Hydrophobic% Polar
43.3156.69
According to VolSite

Ligand :
1qy5_1 Structure
HET Code: NEC
Formula: C12H16N6O4
Molecular weight: 308.293 g/mol
DrugBank ID: DB03719
Buried Surface Area:54.96 %
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
18.973-17.605353.961


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
C52CEMET- 854.490Hydrophobic
N6OD2ASP- 1492.87161.49H-Bond
(Ligand Donor)
C1'SDMET- 1543.550Hydrophobic
N5'OASN- 1623.02129.33H-Bond
(Ligand Donor)
O2'OD1ASN- 1623.06144.58H-Bond
(Ligand Donor)
C4'CBASN- 1624.060Hydrophobic
C1'CBASN- 1624.250Hydrophobic
C4'CD2LEU- 1634.380Hydrophobic
C52CBVAL- 1973.860Hydrophobic
C52CE2TYR- 2003.360Hydrophobic
N1OHOH- 4022.73155.22H-Bond
(Protein Donor)
O5'OHOH- 4032.59179.97H-Bond
(Protein Donor)