scPDB - 5a8e entry

Protein Data Bank Entry:

PDB ID : 5a8e

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2015-07-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-1 adrenergic receptor
ID:	ADRB1_MELGA
AC:	P07700
Organism:	Meleagris gallopavo
Reign:	Eukaryota
TaxID:	9103
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	0.000
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.423	1312.875

% Hydrophobic	% Polar
64.27	35.73
According to VolSite

Ligand :

HET Code:	XTK
Formula:	C17H24N3O2
Molecular weight:	302.391 g/mol
DrugBank ID:	-
Buried Surface Area:	73.19 %
Polar Surface area:	85.65 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
23.753	55.357	14.2128

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
C14	CH2	TRP- 117	3.33	0	Hydrophobic	false
C13	CG2	THR- 118	3.87	0	Hydrophobic	false
O2	OD2	ASP- 121	3.01	152.66	H-Bond (Ligand Donor)	false
O2	OD1	ASP- 121	2.63	138.6	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 121	2.7	154.78	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 121	2.7	0	Ionic (Ligand Cationic)	false
C8	CG2	VAL- 122	4.25	0	Hydrophobic	false
C5	CG2	VAL- 122	4	0	Hydrophobic	false
C6	CG1	VAL- 122	3.53	0	Hydrophobic	false
C9	CG2	VAL- 125	3.95	0	Hydrophobic	false
C5	CB	VAL- 125	3.97	0	Hydrophobic	false
C15	CB	PHE- 201	3.96	0	Hydrophobic	false
C13	CB	PHE- 201	4.06	0	Hydrophobic	false
N3	OG1	THR- 203	3.36	163.81	H-Bond (Protein Donor)	false
N1	OG	SER- 211	3.01	160.52	H-Bond (Ligand Donor)	false
C17	CB	SER- 211	3.8	0	Hydrophobic	false
C17	CB	SER- 215	3.33	0	Hydrophobic	false
C9	CZ3	TRP- 303	4.05	0	Hydrophobic	false
C9	CE2	PHE- 306	3.81	0	Hydrophobic	false
C10	CZ	PHE- 306	3.77	0	Hydrophobic	false
N3	ND2	ASN- 310	3.49	166.24	H-Bond (Protein Donor)	false
C15	CE2	PHE- 325	4.06	0	Hydrophobic	false
O2	ND2	ASN- 329	2.81	162.14	H-Bond (Protein Donor)	false
N2	OD1	ASN- 329	2.76	171.74	H-Bond (Ligand Donor)	false