scPDB - 4j5r entry

Protein Data Bank Entry:

PDB ID : 4j5r

Resolution :1.250 Å

Experimental Method : X-ray

Deposition Date : 2013-02-09

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

Cavity properties

Ligandability	Volume (Å3)
0.227	411.750

% Hydrophobic	% Polar
40.16	59.84
According to VolSite

Ligand :

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

X	Y	Z
3.92786	68.5466	9.30054

Binding mode :

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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
C5N	CB	CYS- 33	4.36	0	Hydrophobic	false
C2N	CG2	ILE- 34	4.36	0	Hydrophobic	false
O1A	N	ILE- 44	2.85	172.05	H-Bond (Protein Donor)	false
C2N	CB	ALA- 45	3.62	0	Hydrophobic	false
O3N	NZ	LYS- 84	3.04	131.52	H-Bond (Protein Donor)	false
C4'	CB	PRO- 118	4.04	0	Hydrophobic	false
C3'	CB	ARG- 119	4.5	0	Hydrophobic	false
O2B	N	GLY- 121	2.85	142.63	H-Bond (Protein Donor)	false
O1B	N	GLY- 123	2.84	140.47	H-Bond (Protein Donor)	false
O2A	N	LEU- 124	2.84	169.02	H-Bond (Protein Donor)	false
O1B	N	ASP- 125	2.99	165.79	H-Bond (Protein Donor)	false
C5N	CB	ASP- 125	4.41	0	Hydrophobic	false
O3'	O	HOH- 313	3.06	154.61	H-Bond (Ligand Donor)	false