1TKT | pdb_00001tkt

CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH GW426318


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.282 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1TKT

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Design of non-nucleoside inhibitors of HIV-1 reverse transcriptase with improved drug resistance properties. 1.

Hopkins, A.L.Ren, J.Milton, J.Hazen, R.J.Chan, J.H.Stuart, D.I.Stammers, D.K.

(2004) J Med Chem 47: 5912-5922

  • DOI: https://doi.org/10.1021/jm040071z
  • Primary Citation Related Structures: 
    1TKT, 1TKZ, 1TL1, 1TL3

  • PubMed Abstract: 

    We have used a structure-based approach to design a novel series of non-nucleoside inhibitors of HIV-1 RT (NNRTIs). Detailed analysis of a wide range of crystal structures of HIV-1 RT-NNRTI complexes together with data on drug resistance mutations has identified factors important for tight binding of inhibitors and resilience to mutations. Using this approach we have designed and synthesized a novel series of quinolone NNRTIs. Crystal structure analysis of four of these compounds in complexes with HIV-1 RT confirms the predicted binding modes. Members of this quinolone series retain high activity against the important resistance mutations in RT at Tyr181Cys and Leu100Ile.


  • Organizational Affiliation
    • Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.

Macromolecule Content 

  • Total Structure Weight: 116.62 kDa 
  • Atom Count: 7,624 
  • Modeled Residue Count: 915 
  • Deposited Residue Count: 1,000 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pol polyproteins [Reverse transcriptase], Chain A560Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: POL
EC: 2.7.7.49
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Pol polyproteins [Reverse transcriptase], Chain B440Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: POL
EC: 2.7.7.49
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
H12 BindingDB:  1TKT IC50: min: 710, max: 1360 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.282 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.2α = 90
b = 115.1β = 90
c = 65.2γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Database references
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary