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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:

4pl3

2.900 Å

X-ray

2014-05-16

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Serine/threonine-protein kinase/endoribonuclease IRE1
ID:ERN1_MOUSE
AC:Q9EQY0
Organism:Mus musculus
Reign:Eukaryota
TaxID:10090
EC Number:2.7.11.1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:30.985
Number of residues:33
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.793432.000

% Hydrophobic% Polar
49.2250.78
According to VolSite

Ligand :
4pl3_1 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:63.56 %
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
21.18327.05938.7606


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
C1'CG1VAL- 5864.280Hydrophobic
O1ANZLYS- 5993.38123.08H-Bond
(Protein Donor)
O1ANZLYS- 5993.380Ionic
(Protein Cationic)
N6OGLU- 6433.07145.69H-Bond
(Ligand Donor)
N1NCYS- 6453.27153.89H-Bond
(Protein Donor)
C2'CG2THR- 6484.190Hydrophobic
O3BNZLYS- 6903.970Ionic
(Protein Cationic)
O3'ND1HIS- 6923.03159.35H-Bond
(Protein Donor)
O3AMG MG- 10032.550Metal Acceptor