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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

2y00

2.500 Å

X-ray

2010-11-30

Interactomes:
Molecular Function:
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
A63 %
B37 %


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

LigandabilityVolume (Å3)
1.3541549.125

% Hydrophobic% Polar
67.5432.46
According to VolSite

Ligand :
2y00_1 Structure
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

XYZ
-5.43991-2.5158614.2662


Binding mode :
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
CAJCGGLU- 1304.490Hydrophobic
CACCGGLU- 1303.810Hydrophobic
CACCBCYS- 1333.670Hydrophobic
CAUCG2VAL- 1344.330Hydrophobic
CAQCD1ILE- 1374.130Hydrophobic
OAFNEARG- 1572.94159.79H-Bond
(Protein Donor)
OAFCZARG- 1573.940Ionic
(Protein Cationic)
CALCDARG- 1573.940Hydrophobic
CAMCG1VAL- 1603.860Hydrophobic
CBCCG1ILE- 1613.450Hydrophobic
CASCG2THR- 1644.070Hydrophobic
CARCBTHR- 1644.310Hydrophobic
CATCG2THR- 1643.760Hydrophobic
CAUCG2VAL- 1654.160Hydrophobic
CABCG2ILE- 1684.040Hydrophobic
CAECD1ILE- 1684.480Hydrophobic
CASCD1ILE- 1684.360Hydrophobic
CABCG2VAL- 1724.420Hydrophobic
CALCBARG- 2053.610Hydrophobic
CARCBALA- 2063.790Hydrophobic
CAKCG2ILE- 2094.30Hydrophobic
CAVCD1ILE- 2093.60Hydrophobic
CADCG2ILE- 2094.220Hydrophobic
CADCBALA- 2103.730Hydrophobic
CAQCD1ILE- 2133.740Hydrophobic
CAECG2ILE- 2134.450Hydrophobic
CAKCD1ILE- 2134.380Hydrophobic
CABCG2ILE- 2144.110Hydrophobic
CABCG1ILE- 2144.240Hydrophobic
CANCG1ILE- 2144.10Hydrophobic
CAACG2ILE- 2183.830Hydrophobic
CANCD1ILE- 2184.410Hydrophobic
CAJCGPRO- 2194.230Hydrophobic
CAOCD1ILE- 2224.160Hydrophobic
CAPCD1ILE- 2224.370Hydrophobic