scPDB - 3gjw entry

Protein Data Bank Entry:

PDB ID : 3gjw

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2009-03-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.300	8.300	8.300	0.000	8.300	1

List of CHEMBLId :

CHEMBL571234

Binding Site :

Uniprot Annotation

Name:	Poly [ADP-ribose] polymerase 1
ID:	PARP1_HUMAN
AC:	P09874
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.4.2.30

Chains:

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

Ligand binding site composition:

B-Factor:	27.072
Number of residues:	25
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.946	988.875

% Hydrophobic	% Polar
44.03	55.97
According to VolSite

Ligand :

HET Code:	GJW
Formula:	C16H18N3O
Molecular weight:	268.334 g/mol
DrugBank ID:	-
Buried Surface Area:	55.67 %
Polar Surface area:	38.47 Å2

Number of
H-Bond Acceptors:	1
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
47.9541	53.0957	9.3859

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
C25	CB	ASP- 105	3.93	0	Hydrophobic	false
O20	N	GLY- 202	2.64	156.49	H-Bond (Protein Donor)	false
O20	OG	SER- 243	3.07	152.78	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 246	3.39	0	Aromatic Face/Face	false
C7	CB	TYR- 246	3.62	0	Hydrophobic	false
C13	CB	TYR- 246	3.43	0	Hydrophobic	false
N22	O	HOH- 358	3.13	152.04	H-Bond (Ligand Donor)	false