3N7H

Crystal structure of Odorant Binding Protein 1 from Anopheles gambiae (AgamOBP1) with DEET (N,N-Diethyl-meta-toluamide) and PEG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Anopheles gambiae odorant binding protein crystal complex with the synthetic repellent DEET: implications for structure-based design of novel mosquito repellents.

Tsitsanou, K.E.Thireou, T.Drakou, C.E.Koussis, K.Keramioti, M.V.Leonidas, D.D.Eliopoulos, E.Iatrou, K.Zographos, S.E.

(2012) Cell.Mol.Life Sci. 69: 283-297

  • DOI: 10.1007/s00018-011-0745-z

  • PubMed Abstract: 
  • Insect odorant binding proteins (OBPs) are the first components of the olfactory system to encounter and bind attractant and repellent odors emanating from various sources for presentation to olfactory receptors, which trigger relevant signal transdu ...

    Insect odorant binding proteins (OBPs) are the first components of the olfactory system to encounter and bind attractant and repellent odors emanating from various sources for presentation to olfactory receptors, which trigger relevant signal transduction cascades culminating in specific physiological and behavioral responses. For disease vectors, particularly hematophagous mosquitoes, repellents represent important defenses against parasitic diseases because they effect a reduction in the rate of contact between the vectors and humans. OBPs are targets for structure-based rational approaches for the discovery of new repellent or other olfaction inhibitory compounds with desirable features. Thus, a study was conducted to characterize the high resolution crystal structure of an OBP of Anopheles gambiae, the African malaria mosquito vector, in complex with N,N-diethyl-m-toluamide (DEET), one of the most effective repellents that has been in worldwide use for six decades. We found that DEET binds at the edge of a long hydrophobic tunnel by exploiting numerous non-polar interactions and one hydrogen bond, which is perceived to be critical for DEET's recognition. Based on the experimentally determined affinity of AgamOBP1 for DEET (K (d) of 31.3 μΜ) and our structural data, we modeled the interactions for this protein with 29 promising leads reported in the literature to have significant repellent activities, and carried out fluorescence binding studies with four highly ranked ligands. Our experimental results confirmed the modeling predictions indicating that structure-based modeling could facilitate the design of novel repellents with enhanced binding affinity and selectivity.


    Organizational Affiliation

    Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, Athens, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Odorant binding protein
A, B
125Anopheles gambiaeMutation(s): 0 
Gene Names: OBP17 (1279770, AgamOBP1)
Find proteins for A0A1U7F4W2 (Anopheles gambiae)
Go to UniProtKB:  A0A1U7F4W2
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
DE3
Query on DE3

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Download CCD File 
A, B
N,N-diethyl-3-methylbenzamide
C12 H17 N O
MMOXZBCLCQITDF-UHFFFAOYSA-N
 Ligand Interaction
MOH
Query on MOH

Download SDF File 
Download CCD File 
A, B
METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEU
Query on PEU

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Download CCD File 
A, B
2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL
PEG 8000
C55 H112 O28
ISGUIIHZEJGUGQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DE3Kd: 31300 nM BINDINGMOAD
DE3Kd: 31300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 55.930α = 90.00
b = 63.540β = 90.00
c = 68.110γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-01-18
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description