3IRX

Crystal Structure of HIV-1 reverse transcriptase (RT) in complex with the Non-nucleoside RT Inhibitor (E)-S-Methyl 5-(1-(3,7-Dimethyl-2-oxo-2,3-dihydrobenzo[d]oxazol-5-yl)-5-(5-methyl-1,3,4-oxadiazol-2-yl)pent-1-enyl)-2-methoxy-3-methylbenzothioate.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of HIV-1 reverse transcriptase (RT) in complex with the alkenyldiarylmethane (ADAM) Non-nucleoside RT Inhibitor (E)-S-Methyl 5-(1-(3,7-Dimethyl-2-oxo-2,3-dihydrobenzo[d]oxazol-5-yl)-5-(5-methyl-1,3,4-oxadiazol-2-yl)pent-1-enyl)-2-methoxy-3-methylbenzothioate.

Cullen, M.D.Ho, W.C.Bauman, J.D.Das, K.Arnold, E.Hartman, T.L.Watson, K.M.Buckheit, R.W.Pannecouque, C.De Clercq, E.Cushman, M.

(2009) J.Med.Chem. 52: 6467-6473

  • DOI: 10.1021/jm901167t
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Two crystal structures have been solved for separate complexes of alkenyldiarylmethane (ADAM) nonnucleoside reverse transcriptase inhibitors (NNRTI) 3 and 4 with HIV-1 reverse transcriptase (RT). The structures reveal inhibitor binding is exclusively ...

    Two crystal structures have been solved for separate complexes of alkenyldiarylmethane (ADAM) nonnucleoside reverse transcriptase inhibitors (NNRTI) 3 and 4 with HIV-1 reverse transcriptase (RT). The structures reveal inhibitor binding is exclusively hydrophobic in nature and the shape of the inhibitor-bound NNRTI binding pocket is unique among other reported inhibitor-RT crystal structures. Primarily, ADAMs 3 and 4 protrude from a large gap in the back side of the binding pocket, placing portions of the inhibitors unusually close to the polymerase active site and allowing 3 to form a weak hydrogen bond with Lys223. The lack of additional stabilizing interactions, beyond the observed hydrophobic surface contacts, between 4 and RT is quite perplexing given the extreme potency of the compound (IC(50)


    Organizational Affiliation

    Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, and Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase/ribonuclease H
A
558Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 3 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase
B
428Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDR
Query on UDR

Download SDF File 
Download CCD File 
A
(E)-S-Methyl 5-(1-(3,7-Dimethyl-2-oxo-2,3-dihydrobenzo[d]oxazol-5-yl)-5-(5-methyl-1,3,4-oxadiazol-2-yl)pent-1-enyl)-2-methoxy-3-methylbenzothioate
S-methyl 5-[(1E)-1-(3,7-dimethyl-2-oxo-2,3-dihydro-1,3-benzoxazol-5-yl)-5-(5-methyl-1,3,4-oxadiazol-2-yl)pent-1-en-1-yl]-2-methoxy-3-methylbenzenecarbothioate
C27 H29 N3 O5 S
OIXOQSQILWVOGS-AWQFTUOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UDRIC50: 1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.236 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 164.639α = 90.00
b = 75.385β = 100.08
c = 110.662γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-08-24 
  • Released Date: 2010-04-07 
  • Deposition Author(s): Ho, W.C., Arnold, E.

Revision History 

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance