scPDB - 2y00 entry

Protein Data Bank Entry:

PDB ID : 2y00

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2010-11-30

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	63 %
B	37 %

Ligand binding site composition:

B-Factor:	21.155
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.354	1549.125

% Hydrophobic	% Polar
67.54	32.46
According to VolSite

Ligand :

HET Code:	Y01
Formula:	C31H49O4
Molecular weight:	485.718 g/mol
DrugBank ID:	-
Buried Surface Area:	55.75 %
Polar Surface area:	66.43 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	0
Rings:	4
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-5.43991	-2.51586	14.2662

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
CAJ	CG	GLU- 130	4.49	0	Hydrophobic	false
CAC	CG	GLU- 130	3.81	0	Hydrophobic	false
CAC	CB	CYS- 133	3.67	0	Hydrophobic	false
CAU	CG2	VAL- 134	4.33	0	Hydrophobic	false
CAQ	CD1	ILE- 137	4.13	0	Hydrophobic	false
OAF	NE	ARG- 157	2.94	159.79	H-Bond (Protein Donor)	false
OAF	CZ	ARG- 157	3.94	0	Ionic (Protein Cationic)	false
CAL	CD	ARG- 157	3.94	0	Hydrophobic	false
CAM	CG1	VAL- 160	3.86	0	Hydrophobic	false
CBC	CG1	ILE- 161	3.45	0	Hydrophobic	false
CAS	CG2	THR- 164	4.07	0	Hydrophobic	false
CAR	CB	THR- 164	4.31	0	Hydrophobic	false
CAT	CG2	THR- 164	3.76	0	Hydrophobic	false
CAU	CG2	VAL- 165	4.16	0	Hydrophobic	false
CAB	CG2	ILE- 168	4.04	0	Hydrophobic	false
CAE	CD1	ILE- 168	4.48	0	Hydrophobic	false
CAS	CD1	ILE- 168	4.36	0	Hydrophobic	false
CAB	CG2	VAL- 172	4.42	0	Hydrophobic	false
CAL	CB	ARG- 205	3.61	0	Hydrophobic	false
CAR	CB	ALA- 206	3.79	0	Hydrophobic	false
CAK	CG2	ILE- 209	4.3	0	Hydrophobic	false
CAV	CD1	ILE- 209	3.6	0	Hydrophobic	false
CAD	CG2	ILE- 209	4.22	0	Hydrophobic	false
CAD	CB	ALA- 210	3.73	0	Hydrophobic	false
CAQ	CD1	ILE- 213	3.74	0	Hydrophobic	false
CAE	CG2	ILE- 213	4.45	0	Hydrophobic	false
CAK	CD1	ILE- 213	4.38	0	Hydrophobic	false
CAB	CG2	ILE- 214	4.11	0	Hydrophobic	false
CAB	CG1	ILE- 214	4.24	0	Hydrophobic	false
CAN	CG1	ILE- 214	4.1	0	Hydrophobic	false
CAA	CG2	ILE- 218	3.83	0	Hydrophobic	false
CAN	CD1	ILE- 218	4.41	0	Hydrophobic	false
CAJ	CG	PRO- 219	4.23	0	Hydrophobic	false
CAO	CD1	ILE- 222	4.16	0	Hydrophobic	false
CAP	CD1	ILE- 222	4.37	0	Hydrophobic	false