1FK9

CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH DMP-266(EFAVIRENZ)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural basis for the resilience of efavirenz (DMP-266) to drug resistance mutations in HIV-1 reverse transcriptase.

Ren, J.Milton, J.Weaver, K.L.Short, S.A.Stuart, D.I.Stammers, D.K.

(2000) STRUCTURE FOLD.DES. 8: 1089-1094

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Efavirenz is a second-generation non-nucleoside inhibitor of HIV-1 reverse transcriptase (RT) that has recently been approved for use against HIV-1 infection. Compared with first-generation drugs such as nevirapine, efavirenz shows greater resilience ...

    Efavirenz is a second-generation non-nucleoside inhibitor of HIV-1 reverse transcriptase (RT) that has recently been approved for use against HIV-1 infection. Compared with first-generation drugs such as nevirapine, efavirenz shows greater resilience to drug resistance mutations within HIV-1 RT. In order to understand the basis for this resilience at the molecular level and to help the design of further-improved anti-AIDS drugs, we have determined crystal structures of efavirenz and nevirapine with wild-type RT and the clinically important K103N mutant.


    Related Citations: 
    • 3'-azido-3'-deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes
      Ren, J.,Esnouf, R.M.,Hopkins, A.L.,Jones, E.Y.,Kirby, I.,Keeling, J.,Ross, C.K.,Larder, B.A.,Stuart, D.I.,Stammers, D.K.
      (1998) Proc.Natl.Acad.Sci.USA 95: 9518
    • Continuous and discontinuous changes in the unit cell of HIV-1 reverse transcriptase crystals on dehydration
      Esnouf, R.M.,Ren, J.,Garman, E.,Somers, D.O.,Ross, C.K.,Jones, E.Y.,Stammers, D.K.,Stuart, D.I.
      (1998) Acta Crystallogr.,Sect.D 54: 938
    • Crystallographic analysis of the binding modes of non-nucleoside thiazoloisoindolinone inhibitors to HIV-1 reverse transcriptase and comparison with modeling studies
      Ren, J.,Esnouf, R.M.,Hopkins, A.L.,Stuart, D.I.,Stammers, D.K.
      (1999) J.Med.Chem. 42: 3845
    • Design of MKC-442 (emivirine) analogues with improved activity against drug-resistant HIV mutants
      Hopkins, A.L.,Ren, J.,Tanaka, H.,Baba, M.,Okamato, M.,Stuart, D.I.,Stammers, D.K.
      (1999) J.Med.Chem. 42: 4500
    • Phenethylthiazolylthiourea (PETT) non-nucleoside inhibitors of HIV-1 and HIV-2 reverse transcriptases: structural and biochemical analyses
      Ren, J.,Diprose, J.,Warren, J.,Esnouf, R.M.,Bird, L.E.,Ikemizu, S.,Slater, M.,Milton, J.,Balzarini, J.,Stuart, D.I.,Stammers, D.K.
      (2000) J.Biol.Chem. 275: 5633
    • Mechanism of Inhibition of HIV-1 Reverse Transcriptase by Non-nucleoside Inhibitors
      Esnouf, R.M.,Ren, J.,Ross, C.K.,Jones, E.Y.,Stammers, D.K.,Stuart, D.I.
      (1995) Nat.Struct.Mol.Biol. 2: 303
    • High Resolution Structures of HIV-1 RT From Four RT-inhibitor Complexes
      Ren, J.,Esnouf, R.M.,Garman, E.,Somers, D.O.,Ross, C.K.,Kirby, I.,Keeling, J.,Darby, G.,Jones, E.Y.,Stuart, D.I.,Stammers, D.K.
      (1995) Nat.Struct.Mol.Biol. 2: 293
    • Unique features in the structure of the complex between HIV-1 reverse transcriptase and the bis(heteroaryl)piperazine (BHAP) U-90152 explain resistance mutations for this non-nucleoside inhibitor
      Esnouf, R.M.,Ren, J.,Hopkins, A.L.,Ross, C.K.,Jones, E.Y.,Stammers, D.K.,Stuart, D.I.
      (1997) Proc.Natl.Acad.Sci.USA 94: 3984
    • Binding of the second generattion non-nucleoside inhibitor S-1153 to HIV-1 reverse transcriptase involves extensive main chain hydrogen bonding
      Ren, J.,Nichols, C.,Bird, L.E.,Fujiwara, T.,Suginoto, H.,Stuart, D.I.,Stammers, D.K.
      (2000) J.Biol.Chem. 275: 14316
    • Crystals of HIV-1 Reverse Transcriptase Diffracting to 2.2 Angstrom Resolution
      Stammers, D.K.,Somers, D.O.,Ross, C.K.,Kirby, I.,Ray, P.H.,Wilson, J.E.,Norman, M.,Ren, J.,Esnouf, R.M.,Garman, E.,Jones, E.Y.,Stuart, D.I.
      (1994) J.Mol.Biol. 242: 586
    • Crystal structures of reverse transcriptase in complex with carboxanilide derivatives
      Ren, J.,Esnouf, R.M.,Hopkins, A.L.,Warren, J.,Balzarini, J.,Stuart, D.I.,Stammers, D.K.
      (1998) Biochemistry 37: 14394
    • Complexes of HIV-1 reverse transcriptase with inhibitors of the HEPT series reveal conformational changes relevant to the design of potent non-nucleoside inhibitors
      L Hopkins, A.,Ren, J.,Esnouf, R.M.,Willcox, B.E.,Jones, E.Y.,Ross, C.K.,Miyasaka, T.,Walker, R.T.,Tanaka, H.,Stammers, D.K.,Stuart, D.I.
      (1996) J.Med.Chem. 39: 1589
    • The structure of HIV-1 reverse transcriptase complexed with 9-chloro-TIBO: lessons for inhibitor design
      Ren, J.,Esnouf, R.M.,Hopkins, A.L.,Ross, C.K.,Jones, E.Y.,K Stammers, D.,Stuart, D.I.
      (1995) Structure 3: 915


    Organizational Affiliation

    Structural Biology Division The Wellcome Trust Centre for Human Genetics University of Oxford OX3 7BN, Oxford, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 RT, A-CHAIN
A
543Human 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 RT, B-CHAIN
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
EFZ
Query on EFZ

Download SDF File 
Download CCD File 
A
(-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE
DMP-266; Efavirenz
C14 H9 Cl F3 N O2
XPOQHMRABVBWPR-ZDUSSCGKSA-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 %)
EFZEC50: 1 - 300 nM (99) BINDINGDB
EFZKi: 3 - 380 nM (99) BINDINGDB
EFZIC50: 0.8 - 3400 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 139.800α = 90.00
b = 115.000β = 90.00
c = 65.400γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-07-18
    Type: Non-polymer description
  • Version 1.4: 2017-02-01
    Type: Structure summary