scPDB - 2ada entry

Protein Data Bank Entry:

PDB ID : 2ada

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 1994-12-02

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_MOUSE
AC:	P03958
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	3.5.4.4

Chains:

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

Ligand binding site composition:

B-Factor:	9.891
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.958	459.000

% Hydrophobic	% Polar
55.88	44.12
According to VolSite

Ligand :

HET Code:	HPR
Formula:	C10H14N4O5
Molecular weight:	270.242 g/mol
DrugBank ID:	DB02472
Buried Surface Area:	79.96 %
Polar Surface area:	131.2 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
5.09905	19.6348	37.4253

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
O5'	ND1	HIS- 17	2.82	136.77	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 19	3	152.78	H-Bond (Ligand Donor)	false
O5'	OD1	ASP- 19	2.61	139.31	H-Bond (Ligand Donor)	false
O5'	OD2	ASP- 19	3.16	154.75	H-Bond (Ligand Donor)	false
C6	CD1	LEU- 58	4.48	0	Hydrophobic	false
C6	CE2	PHE- 61	3.77	0	Hydrophobic	false
C2'	CD2	LEU- 62	3.72	0	Hydrophobic	false
C2'	CZ	PHE- 65	3.72	0	Hydrophobic	false
C3'	CE2	PHE- 65	3.99	0	Hydrophobic	false
C5'	CB	SER- 103	4.29	0	Hydrophobic	false
C3'	CD1	LEU- 106	4.5	0	Hydrophobic	false
C5'	SG	CYS- 153	4.09	0	Hydrophobic	false
C4'	CE	MET- 155	3.69	0	Hydrophobic	false
C1'	CB	ALA- 183	3.99	0	Hydrophobic	false
C4'	CB	ALA- 183	4.38	0	Hydrophobic	false
N3	N	GLY- 184	3.16	160.23	H-Bond (Protein Donor)	false
N1	OE2	GLU- 217	3.32	139.14	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 217	2.81	163.39	H-Bond (Ligand Donor)	false
O6	NE2	HIS- 238	3.24	150.11	H-Bond (Protein Donor)	false
O6	OD1	ASP- 295	2.67	141.65	H-Bond (Ligand Donor)	false
O6	ZN	ZN- 400	2.29	0	Metal Acceptor	false
DuAr	ZN	ZN- 400	3.91	145.49	Pi/Cation	false