scPDB - 1ndy entry

Protein Data Bank Entry:

PDB ID : 1ndy

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2002-12-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenosine deaminase
ID:	ADA_BOVIN
AC:	P56658
Organism:	Bos taurus
Reign:	Eukaryota
TaxID:	9913
EC Number:	3.5.4.4

Chains:

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

Ligand binding site composition:

B-Factor:	15.909
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.083	722.250

% Hydrophobic	% Polar
58.88	41.12
According to VolSite

Ligand :

HET Code:	FR3
Formula:	C18H19N3O2
Molecular weight:	309.362 g/mol
DrugBank ID:	DB03572
Buried Surface Area:	63.43 %
Polar Surface area:	81.14 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
49.3947	54.9652	19.7843

Binding mode :

What is Poseview ?

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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
O15	ND1	HIS- 17	2.83	165.97	H-Bond (Protein Donor)	false
DuAr	DuAr	HIS- 17	3.61	0	Aromatic Face/Face	false
O15	OD2	ASP- 19	2.69	174.32	H-Bond (Ligand Donor)	false
O15	OD1	ASP- 19	3.39	123.7	H-Bond (Ligand Donor)	false
C6	CD1	LEU- 58	3.86	0	Hydrophobic	false
C28	CD2	LEU- 62	3.22	0	Hydrophobic	false
C28	CD2	LEU- 62	3.22	0	Hydrophobic	false
C13	CE2	PHE- 65	4.42	0	Hydrophobic	false
C19	CZ	PHE- 65	3.91	0	Hydrophobic	false
C14	CB	SER- 103	4.46	0	Hydrophobic	false
C13	CD1	LEU- 106	4.34	0	Hydrophobic	false
C18	CD1	LEU- 106	3.61	0	Hydrophobic	false
C25	CD1	LEU- 106	3.61	0	Hydrophobic	false
C14	SD	MET- 155	4.48	0	Hydrophobic	false
C22	CE	MET- 155	3.69	0	Hydrophobic	false
C25	CE	MET- 155	3.7	0	Hydrophobic	false
C2	CB	ASP- 185	4.17	0	Hydrophobic	false
N10	OD2	ASP- 296	2.99	158.41	H-Bond (Ligand Donor)	false