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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:

4j5r

1.250 Å

X-ray

2013-02-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:O-acetyl-ADP-ribose deacetylase 1
ID:OARD1_HUMAN
AC:Q9Y530
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:3.5.1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:9.217
Number of residues:39
Including
Standard Amino Acids: 36
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals: CL

Cavity properties

LigandabilityVolume (Å3)
0.227411.750

% Hydrophobic% Polar
40.1659.84
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median4j5rHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy80204060Highcharts.com
Ligand :
4j5r_1 Structure
HET Code: A1R
Formula: C15H23N6O12P2
Molecular weight: 541.324 g/mol
DrugBank ID: -
Buried Surface Area:54.25 %
Polar Surface area: 303.95 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 6
Rings: 4
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 9

Mass center Coordinates

XYZ
3.9278668.54669.30054
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median4j5rRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation801020Highcharts.com


Binding mode :
What is Poseview ?
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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
C5NCBCYS- 334.360Hydrophobic
C2NCG2ILE- 344.360Hydrophobic
O1ANILE- 442.85172.05H-Bond
(Protein Donor)
C2NCBALA- 453.620Hydrophobic
O3NNZLYS- 843.04131.52H-Bond
(Protein Donor)
C4'CBPRO- 1184.040Hydrophobic
C3'CBARG- 1194.50Hydrophobic
O2BNGLY- 1212.85142.63H-Bond
(Protein Donor)
O1BNGLY- 1232.84140.47H-Bond
(Protein Donor)
O2ANLEU- 1242.84169.02H-Bond
(Protein Donor)
O1BNASP- 1252.99165.79H-Bond
(Protein Donor)
C5NCBASP- 1254.410Hydrophobic
O3'OHOH- 3133.06154.61H-Bond
(Ligand Donor)