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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:

2o1v

2.450 Å

X-ray

2006-11-29

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
B100 %


Ligand binding site composition:

B-Factor:31.159
Number of residues:30
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.232388.125

% Hydrophobic% Polar
46.9653.04
According to VolSite

Ligand :
2o1v_2 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:46.29 %
Polar Surface area: 260.7 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-14.418141.882353.6379


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
O2AND2ASN- 1073.4135.81H-Bond
(Protein Donor)
N6OD2ASP- 1493.09165.2H-Bond
(Ligand Donor)
C1'SDMET- 1544.060Hydrophobic
C4'CBASN- 1624.180Hydrophobic
C1'CBASN- 1623.90Hydrophobic
O1ANPHE- 1992.76172.59H-Bond
(Protein Donor)
C5'CBPHE- 1993.80Hydrophobic
N6OG1THR- 2453.1122.56H-Bond
(Ligand Donor)
O1BMG MG- 7552.280Metal Acceptor
O3BMG MG- 7552.630Metal Acceptor