scPDB - 4b1i entry

Protein Data Bank Entry:

PDB ID : 4b1i

Resolution :2.140 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:	33.594
Number of residues:	46
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.872	604.125

% Hydrophobic	% Polar
57.54	42.46
According to VolSite

Ligand :

HET Code:	A8P
Formula:	C23H40N7O12P2
Molecular weight:	668.551 g/mol
DrugBank ID:	-
Buried Surface Area:	66.41 %
Polar Surface area:	315.98 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
28.3125	-1.21934	2.46659

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
N14	N	ILE- 726	3.37	173.06	H-Bond (Protein Donor)	false
N44	OE1	GLU- 727	2.89	141.81	H-Bond (Ligand Donor)	false
C19	CE2	PHE- 738	4.12	0	Hydrophobic	false
C22	CE2	PHE- 738	4.22	0	Hydrophobic	false
C24	CD2	PHE- 738	3.88	0	Hydrophobic	false
O41	ND2	ASN- 740	3.09	168.27	H-Bond (Protein Donor)	false
C36	CB	ASN- 740	3.82	0	Hydrophobic	false
C7	CB	VAL- 753	3.85	0	Hydrophobic	false
O28	N	GLN- 754	3.01	151.32	H-Bond (Protein Donor)	false
C37	CB	GLU- 755	3.88	0	Hydrophobic	false
O40	OE1	GLU- 755	2.62	161.26	H-Bond (Ligand Donor)	false
C5	CE1	TYR- 795	4.07	0	Hydrophobic	false
C6	CG	TYR- 795	3.36	0	Hydrophobic	false
C7	CB	TYR- 795	3.96	0	Hydrophobic	false
C4	CZ	TYR- 795	4.03	0	Hydrophobic	false
C19	CB	ASN- 869	4.32	0	Hydrophobic	false
C22	CB	ASN- 869	3.81	0	Hydrophobic	false
O43	ND2	ASN- 869	3.1	166.29	H-Bond (Protein Donor)	false
O31	N	GLY- 871	3.01	124.74	H-Bond (Protein Donor)	false
O32	N	GLY- 873	2.95	155.17	H-Bond (Protein Donor)	false
O27	N	ALA- 874	2.81	170.29	H-Bond (Protein Donor)	false
O32	N	PHE- 875	3.01	158.58	H-Bond (Protein Donor)	false
C34	CZ	PHE- 875	3.81	0	Hydrophobic	false
C36	CZ	PHE- 875	3.61	0	Hydrophobic	false
C1	CD2	PHE- 902	3.86	0	Hydrophobic	false
C4	CE2	PHE- 902	3.92	0	Hydrophobic	false
C6	CE2	PHE- 902	4.32	0	Hydrophobic	false
C19	CG	PHE- 902	4.06	0	Hydrophobic	false
C20	CD2	PHE- 902	3.52	0	Hydrophobic	false
O31	O	HOH- 2330	2.89	179.98	H-Bond (Protein Donor)	false
N16	O	HOH- 2436	2.75	179.97	H-Bond (Protein Donor)	false