scPDB - 4b1h entry

Protein Data Bank Entry:

PDB ID : 4b1h

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2012-07-10

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_HUMAN
AC:	Q86W56
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.2.1.143

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	26.212
Number of residues:	46
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.516	523.125

% Hydrophobic	% Polar
45.16	54.84
According to VolSite

Ligand :

HET Code:	AR6
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	DB02059
Buried Surface Area:	72.16 %
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
27.817	-1.17456	3.63936

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- 726	3.43	176.86	H-Bond (Protein Donor)	false
N6	OE1	GLU- 727	2.97	144.51	H-Bond (Ligand Donor)	false
C1'	CE2	PHE- 738	4.33	0	Hydrophobic	false
C4'	CE2	PHE- 738	4.38	0	Hydrophobic	false
C5'	CD2	PHE- 738	3.89	0	Hydrophobic	false
O3D	ND2	ASN- 740	2.96	160.81	H-Bond (Protein Donor)	false
C3D	CB	ASN- 740	3.64	0	Hydrophobic	false
C1D	CG2	VAL- 753	3.57	0	Hydrophobic	false
O1A	N	GLN- 754	2.82	147.15	H-Bond (Protein Donor)	false
C2D	CB	GLU- 755	4.06	0	Hydrophobic	false
O2D	OE1	GLU- 755	2.61	159.98	H-Bond (Ligand Donor)	false
O1D	OE1	GLU- 756	3.26	137.89	H-Bond (Ligand Donor)	false
O1D	OE2	GLU- 756	2.58	158.81	H-Bond (Ligand Donor)	false
C3'	CZ	TYR- 795	4.45	0	Hydrophobic	false
O2'	ND2	ASN- 869	3.03	163.63	H-Bond (Protein Donor)	false
C4'	CB	ASN- 869	3.7	0	Hydrophobic	false
C1'	CB	ASN- 869	4.04	0	Hydrophobic	false
O1B	N	GLY- 871	2.91	128.2	H-Bond (Protein Donor)	false
O2B	N	GLY- 873	2.93	151.55	H-Bond (Protein Donor)	false
O2A	N	ALA- 874	2.91	172.13	H-Bond (Protein Donor)	false
C4D	CB	ALA- 874	3.91	0	Hydrophobic	false
O2B	N	PHE- 875	3.18	153.82	H-Bond (Protein Donor)	false
C3D	CZ	PHE- 875	3.66	0	Hydrophobic	false
C4D	CE1	PHE- 875	3.59	0	Hydrophobic	false
C5D	CD2	PHE- 875	3.82	0	Hydrophobic	false
C1'	CG	PHE- 902	3.97	0	Hydrophobic	false
C2'	CD2	PHE- 902	3.47	0	Hydrophobic	false
O1B	O	HOH- 2266	2.79	154.02	H-Bond (Protein Donor)	false
N3	O	HOH- 2339	2.64	166.09	H-Bond (Protein Donor)	false