scPDB - 2l8r entry

Protein Data Bank Entry:

PDB ID : 2l8r

Resolution : Å

Experimental Method : NMR

Deposition Date : 2011-01-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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
A	100 %

Ligand binding site composition:

B-Factor:	37.189
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.024	553.500

% Hydrophobic	% Polar
51.83	48.17
According to VolSite

Ligand :

HET Code:	APR
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	-
Buried Surface Area:	66.2 %
Polar Surface area:	316.8 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
2.81797	-5.48117	-7.827

Binding mode :

What is Poseview ?

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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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
N1	N	LEU- 21	2.66	164.66	H-Bond (Protein Donor)	false
C5D	CB	CYS- 33	4.33	0	Hydrophobic	false
C2D	CB	ILE- 34	4.47	0	Hydrophobic	false
O1D	O	ALA- 42	3.46	175.64	H-Bond (Ligand Donor)	false
C5'	CG2	ILE- 44	3.34	0	Hydrophobic	false
C5'	CB	PRO- 118	3.64	0	Hydrophobic	false
C4'	CB	ARG- 119	4.33	0	Hydrophobic	false
O1B	N	GLY- 121	2.69	152.46	H-Bond (Protein Donor)	false
C1D	CB	LEU- 124	4.38	0	Hydrophobic	false
C4D	CB	ASP- 125	3.72	0	Hydrophobic	false
C1'	CB	LEU- 152	3.71	0	Hydrophobic	false
O2'	OXT	LEU- 152	2.85	141.85	H-Bond (Ligand Donor)	false