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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:

1gt5

2.080 Å

X-ray

2002-01-10

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Odorant-binding protein
ID:OBP_BOVIN
AC:P07435
Organism:Bos taurus
Reign:Eukaryota
TaxID:9913
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:29.007
Number of residues:24
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.837459.000

% Hydrophobic% Polar
78.6821.32
According to VolSite

Ligand :
1gt5_1 Structure
HET Code: BZQ
Formula: C13H10O
Molecular weight: 182.218 g/mol
DrugBank ID: DB01878
Buried Surface Area:66.46 %
Polar Surface area: 17.07 Å2
Number of
H-Bond Acceptors: 1
H-Bond Donors: 0
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-0.317-1.032646.48314


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
C10CD1ILE- 224.260Hydrophobic
C11CG2ILE- 224.260Hydrophobic
OOG1THR- 382.82147.99H-Bond
(Protein Donor)
C1CG2VAL- 694.340Hydrophobic
C2CG1VAL- 694.170Hydrophobic
C2CBTYR- 833.950Hydrophobic
C3CBASN- 874.390Hydrophobic
C13CBALA- 1014.040Hydrophobic
C12CBASN- 1033.940Hydrophobic
C13CBASN- 1033.650Hydrophobic
C11CBLEU- 1153.750Hydrophobic