scPDB - 4na4 entry

Protein Data Bank Entry:

PDB ID : 4na4

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2013-10-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Poly(ADP-ribose) glycohydrolase
ID:	PARG_MOUSE
AC:	O88622
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	3.2.1.143

Chains:

Chain Name:	Percentage of Residues within binding site
A	95 %
C	5 %

Ligand binding site composition:

B-Factor:	41.267
Number of residues:	46
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.691	877.500

% Hydrophobic	% Polar
41.92	58.08
According to VolSite

Ligand :

HET Code:	A1R
Formula:	C15H23N6O12P2
Molecular weight:	541.324 g/mol
DrugBank ID:	-
Buried Surface Area:	71.24 %
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
54.4787	38.6737	21.3804

Binding mode :

What is Poseview ?

2D View
3D View

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	ILE- 719	3.21	172.86	H-Bond (Protein Donor)	false
N6	OE1	GLU- 720	2.92	150.43	H-Bond (Ligand Donor)	false
C1'	CE2	PHE- 731	4.26	0	Hydrophobic	false
C4'	CE2	PHE- 731	4.14	0	Hydrophobic	false
C5'	CD2	PHE- 731	3.68	0	Hydrophobic	false
O3N	ND2	ASN- 733	2.94	170.41	H-Bond (Protein Donor)	false
C3N	CB	ASN- 733	3.96	0	Hydrophobic	false
O1A	N	GLN- 747	3.1	146.89	H-Bond (Protein Donor)	false
O2N	OE1	GLU- 748	3	167.74	H-Bond (Ligand Donor)	false
C2N	CB	GLU- 748	4.13	0	Hydrophobic	false
C3'	CZ	TYR- 788	4.4	0	Hydrophobic	false
C1'	CB	ASN- 862	4.49	0	Hydrophobic	false
C4'	CB	ASN- 862	3.89	0	Hydrophobic	false
O2'	ND2	ASN- 862	3.42	158.29	H-Bond (Protein Donor)	false
O2B	N	GLY- 864	3.06	124.76	H-Bond (Protein Donor)	false
O1B	N	GLY- 866	2.88	145.17	H-Bond (Protein Donor)	false
O2A	N	ALA- 867	2.72	160.02	H-Bond (Protein Donor)	false
C5N	CB	ALA- 867	4.39	0	Hydrophobic	false
O1B	N	PHE- 868	3.05	163.02	H-Bond (Protein Donor)	false
C5N	CD1	PHE- 868	3.61	0	Hydrophobic	false
C3N	CZ	PHE- 868	3.65	0	Hydrophobic	false
C1'	CG	PHE- 895	3.92	0	Hydrophobic	false
C2'	CD2	PHE- 895	3.58	0	Hydrophobic	false
N3	O	HOH- 1102	2.71	179.96	H-Bond (Protein Donor)	false
O2B	O	HOH- 1110	2.62	179.96	H-Bond (Protein Donor)	false