scPDB - 3i9j entry

Protein Data Bank Entry:

PDB ID : 3i9j

Resolution :2.180 Å

Experimental Method : X-ray

Deposition Date : 2009-07-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
ID:	NADA_APLCA
AC:	P29241
Organism:	Aplysia californica
Reign:	Eukaryota
TaxID:	6500
EC Number:	3.2.2.6

Chains:

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

Ligand binding site composition:

B-Factor:	15.764
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.074	293.625

% Hydrophobic	% Polar
50.57	49.43
According to VolSite

Ligand :

HET Code:	NFD
Formula:	C21H25FN7O14P2
Molecular weight:	680.408 g/mol
DrugBank ID:	-
Buried Surface Area:	48.79 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
4.67807	5.08542	18.6862

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
C2'N	CZ2	TRP- 77	3.7	0	Hydrophobic	false
C5'N	CH2	TRP- 77	3.66	0	Hydrophobic	false
C3'N	CE2	TRP- 77	3.36	0	Hydrophobic	false
O3'N	N	TRP- 77	3.29	167.12	H-Bond (Protein Donor)	false
O1A	N	GLY- 79	2.51	148.07	H-Bond (Protein Donor)	false
C4N	CB	TRP- 140	3.86	0	Hydrophobic	false
F2A	CE1	PHE- 174	4.06	0	Hydrophobic	false
C5N	CB	PHE- 174	4.02	0	Hydrophobic	false
C5N	CD2	PHE- 174	3.28	0	Hydrophobic	false
C4'N	CB	PHE- 174	4.12	0	Hydrophobic	false
O2N	N	PHE- 174	2.78	151.09	H-Bond (Protein Donor)	false
O1N	N	PHE- 175	3.26	150.14	H-Bond (Protein Donor)	false
O2'N	OE2	GLU- 179	3.1	153.23	H-Bond (Ligand Donor)	false
O3'N	OE1	GLU- 179	2.62	145.61	H-Bond (Ligand Donor)	false
O2'N	O	HOH- 265	3.18	151.71	H-Bond (Protein Donor)	false