4I2Q

Crystal structure of K103N/Y181C mutant of HIV-1 reverse transcriptase in complex with rilpivirine (TMC278) analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.215 

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Ligand Structure Quality Assessment 


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Literature

A comparison of the ability of rilpivirine (TMC278) and selected analogues to inhibit clinically relevant HIV-1 reverse transcriptase mutants.

Johnson, B.C.Pauly, G.T.Rai, G.Patel, D.Bauman, J.D.Baker, H.L.Das, K.Schneider, J.P.Maloney, D.J.Arnold, E.Thomas, C.J.Hughes, S.H.

(2012) Retrovirology 9: 99-99

  • DOI: https://doi.org/10.1186/1742-4690-9-99
  • Primary Citation of Related Structures:  
    4I2P, 4I2Q

  • PubMed Abstract: 

    The recently approved anti-AIDS drug rilpivirine (TMC278, Edurant) is a nonnucleoside inhibitor (NNRTI) that binds to reverse transcriptase (RT) and allosterically blocks the chemical step of DNA synthesis. In contrast to earlier NNRTIs, rilpivirine retains potency against well-characterized, clinically relevant RT mutants. Many structural analogues of rilpivirine are described in the patent literature, but detailed analyses of their antiviral activities have not been published. This work addresses the ability of several of these analogues to inhibit the replication of wild-type (WT) and drug-resistant HIV-1.


  • Organizational Affiliation

    HIV Drug Resistance Program, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, MD 21702-1201, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gag-Pol polyprotein557Human immunodeficiency virus type 1 BH10Mutation(s): 5 
Gene Names: gag-pol
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.1.13.2 (PDB Primary Data)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gag-Pol polyprotein428Human immunodeficiency virus type 1 BH10Mutation(s): 1 
Gene Names: gag-pol
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.1.13.2 (PDB Primary Data)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1BT
Query on 1BT

Download Ideal Coordinates CCD File 
C [auth A](2E)-3-(4-{[6-(1,3-benzothiazol-5-ylamino)-9H-purin-2-yl]amino}-3,5-dimethylphenyl)prop-2-enenitrile
C23 H18 N8 S
FZDPEDQCVGYRLP-ONEGZZNKSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.602α = 90
b = 72.953β = 100.7
c = 108.543γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations