1RT2

CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH TNK-651


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Complexes of HIV-1 reverse transcriptase with inhibitors of the HEPT series reveal conformational changes relevant to the design of potent non-nucleoside inhibitors.

Hopkins, A.L.Ren, J.Esnouf, R.M.Willcox, B.E.Jones, E.Y.Ross, C.Miyasaka, T.Walker, R.T.Tanaka, H.Stammers, D.K.Stuart, D.I.

(1996) J.Med.Chem. 39: 1589-1600

  • DOI: 10.1021/jm960056x
  • Primary Citation of Related Structures:  
  • Also Cited By: 1DTT, 1DTQ

  • PubMed Abstract: 
  • Crystal structures of HIV-1 reverse transcriptase (RT) complexed with a range of chemically diverse non-nucleoside inhibitors (NNIs) have shown a single pocket in which the inhibitors bind and details of the inhibitor-protein interactions. To delinea ...

    Crystal structures of HIV-1 reverse transcriptase (RT) complexed with a range of chemically diverse non-nucleoside inhibitors (NNIs) have shown a single pocket in which the inhibitors bind and details of the inhibitor-protein interactions. To delineate the structural requirements for an effective inhibitor, we have determined the structures of three closely related NNIs which vary widely in their potencies. Crystal structures of HIV-1 RT complexed with two very potent inhibitors, MKC-442 and TNK-651, at 2.55 angstroms resolution complement our previous analysis of the complex with the less effective inhibitor, HEPT. These structures reveal conformational changes which correlate with changes in potency. We suggest that a major determinant of increased potency in the analogues of HEPT is an improved interaction between residue Tyr181 in the protein and the 6-benzyl ring of the inhibitors which stabilizes the structure of the complex. This arises through a conformational switching of the protein structure triggered by the steric bulk of the 5-substituent of the inhibitor pyrimidine ring.


    Related Citations: 
    • Crystals of HIV-1 Reverse Transcriptase Diffracting to 2.2 A Resolution
      Stammers, D.K.,Somers, D.O.,Ross, C.K.,Kirby, I.,Ray, P.H.,Wilson, J.E.,Norman, M.,Ren, J.S.,Esnouf, R.M.,Garman, E.F.
      (1994) J.Mol.Biol. 242: 586
    • The Structure of HIV-1 Reverse Transcriptase Complexed with 9-Chloro-TIBO: Lessons for Inhibitor Design
      Ren, J.,Esnouf, R.,Hopkins, A.,Ross, C.,Jones, Y.,Stammers, D.,Stuart, D.
      (1995) Structure 3: 915
    • High Resolution Structures of HIV-1 RT from Four RT-Inhibitor Complexes
      Ren, J.,Esnouf, R.,Garman, E.,Somers, D.,Ross, C.,Kirby, I.,Keeling, J.,Darby, G.,Jones, Y.,Stuart, D.
      (1995) Nat.Struct.Mol.Biol. 2: 293
    • Mechanism of Inhibition of HIV-1 Reverse Transcriptase by Non-Nucleoside Inhibitors
      Esnouf, R.,Ren, J.,Ross, C.,Jones, Y.,Stammers, D.,Stuart, D.
      (1995) Nat.Struct.Mol.Biol. 2: 303


    Organizational Affiliation

    Laboratory of Molecular Biophysics, Rex Richards Building, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE
A
560Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE
B
440Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TNK
Query on TNK

Download SDF File 
Download CCD File 
A
6-BENZYL-1-BENZYLOXYMETHYL-5-ISOPROPYL URACIL
C22 H24 N2 O3
KSAAUHMSLCPIEX-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TNKIC50: 6 nM (99) BINDINGDB
TNKIC50: 6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 137.300α = 90.00
b = 110.200β = 90.00
c = 72.100γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORphasing
X-PLORmodel building
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-04-21
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-11
    Type: Data collection, Database references, Other