scPDB - 4ldl entry

Protein Data Bank Entry:

PDB ID : 4ldl

Resolution :3.100 Å

Experimental Method : X-ray

Deposition Date : 2013-06-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-2 adrenergic receptor
ID:	ADRB2_HUMAN
AC:	P07550
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

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

Cavity properties

Ligandability	Volume (Å3)
0.611	1829.250

% Hydrophobic	% Polar
42.25	57.75
According to VolSite

Ligand :

HET Code:	XQC
Formula:	C18H24NO4
Molecular weight:	318.387 g/mol
DrugBank ID:	-
Buried Surface Area:	68.23 %
Polar Surface area:	97.53 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	5
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
-3.31309	-13.1052	-50.8831

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
CAD	CH2	TRP- 1109	4.45	0	Hydrophobic	false
CAA	CG2	THR- 1110	4.12	0	Hydrophobic	false
CAA	CB	ASP- 1113	4.49	0	Hydrophobic	false
NAL	OD2	ASP- 1113	2.97	152.58	H-Bond (Ligand Donor)	false
OAO	OD2	ASP- 1113	3.36	145.08	H-Bond (Ligand Donor)	false
OAO	OD1	ASP- 1113	2.79	146.1	H-Bond (Ligand Donor)	false
NAL	OD2	ASP- 1113	2.97	0	Ionic (Ligand Cationic)	false
CAS	CG1	VAL- 1114	4.17	0	Hydrophobic	false
CAU	CG2	VAL- 1114	4.29	0	Hydrophobic	false
CAR	CG1	VAL- 1117	3.7	0	Hydrophobic	false
CAA	CD1	PHE- 1193	3.9	0	Hydrophobic	false
CAC	CG	PHE- 1193	3.43	0	Hydrophobic	false
CAG	CB	PHE- 1193	3.78	0	Hydrophobic	false
OAV	OG	SER- 1203	3.37	153.12	H-Bond (Ligand Donor)	false
OAT	OG	SER- 1207	3.2	157.54	H-Bond (Ligand Donor)	false
CAN	CZ	PHE- 1289	3.63	0	Hydrophobic	false
CAC	CE2	TYR- 1308	3.78	0	Hydrophobic	false
CAJ	CG1	ILE- 1309	3.69	0	Hydrophobic	false
NAL	OD1	ASN- 1312	2.71	175.72	H-Bond (Ligand Donor)	false
OAO	ND2	ASN- 1312	2.88	173.51	H-Bond (Protein Donor)	false
NAL	OH	TYR- 1316	3.42	141.91	H-Bond (Ligand Donor)	false