1FKP

CRYSTAL STRUCTURE OF NNRTI RESISTANT K103N MUTANT HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.5 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 8: 1089-1094

  • DOI: 10.1016/s0969-2126(00)00513-x
  • Primary Citation of Related Structures:  
    1FKP, 1FKO, 1FK9

  • 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 to ...

    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: 
    • 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
    • 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
    • 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
    • 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
    • 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 U S A 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., K Stammers, D., Stuart, D.I.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 938
    • 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 U S A 94: 3984
    • 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., Stammers, D.K., Stuart, D.I.
      (1995) Structure 3: 915
    • 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 Biol 2: 293
    • 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 Biol 2: 303
    • 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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 RT, A-CHAIN A543Human immunodeficiency virus 1Mutation(s): 1 
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 RT, B-CHAIN B440Human immunodeficiency virus 1Mutation(s): 1 
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NVP
Query on NVP

Download Ideal Coordinates CCD File 
A
11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE
C15 H14 N4 O
NQDJXKOVJZTUJA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
AL-PEPTIDE LINKINGC3 H7 N O4 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NEVKi:  2000   nM  BindingDB
NEVIC50:  1480   nM  BindingDB
NEVEC50:  20   nM  BindingDB
NEVEC50:  26   nM  BindingDB
NEVIC50:  1300   nM  BindingDB
NEVEC50:  3900   nM  BindingDB
NEVIC50:  2110   nM  BindingDB
NEVIC50:  1850   nM  BindingDB
NEVIC50:  1900   nM  BindingDB
NEVIC50:  3200   nM  BindingDB
NEVIC50:  84   nM  BindingDB
NEVIC50:  3000   nM  BindingDB
NEVIC50:  3100   nM  BindingDB
NEVEC50:  52   nM  BindingDB
NEVEC50:  53   nM  BindingDB
NEVIC50:  2800   nM  BindingDB
NEVKi:  7000   nM  BindingDB
NEVEC50:  30   nM  BindingDB
NEVIC50:  3930   nM  BindingDB
NEVIC50:  3800   nM  BindingDB
NEVEC50:  7500   nM  BindingDB
NEVIC50:  3500   nM  BindingDB
NEVKi:  7000   nM  BindingDB
NEVEC50:  110   nM  BindingDB
NEVIC50:  300   nM  BindingDB
NEVIC50:  320   nM  BindingDB
NEVEC50:  100   nM  BindingDB
NEVIC50:  500   nM  BindingDB
NEVKi:  10000   nM  BindingDB
NEVIC50:  430   nM  BindingDB
NEVKi:  9000   nM  BindingDB
NEVEC50:  70   nM  BindingDB
NEVIC50:  20000   nM  BindingDB
NEVIC50:  690   nM  BindingDB
NEVIC50:  700   nM  BindingDB
NEVIC50:  600   nM  BindingDB
NEVIC50:  640   nM  BindingDB
NEVIC50:  1100   nM  BindingDB
NEVIC50:  860   nM  BindingDB
NEVKi:  18000   nM  BindingDB
NEVIC50:  101   nM  BindingDB
NEVEC50:  380   nM  BindingDB
NEVIC50:  84   nM  BindingDB
NEVIC50:  23000   nM  BindingDB
NEVIC50:  80   nM  BindingDB
NEVEC50:  250   nM  BindingDB
NEVIC50:  100   nM  BindingDB
NEVKi:  36000   nM  BindingDB
NEVIC50:  200   nM  BindingDB
NEVIC50:  170   nM  BindingDB
NEVIC50:  1700   nM  BindingDB
NEVIC50:  180   nM  BindingDB
NEVIC50:  270   nM  BindingDB
NEVIC50:  250   nM  BindingDB
NEVIC50:  230   nM  BindingDB
NEVIC50:  2600   nM  BindingDB
NEVIC50:  2.5999999046325684   nM  BindingDB
NEVIC50:  6440   nM  BindingDB
NEVIC50:  6650   nM  BindingDB
NEVIC50:  6000   nM  BindingDB
NEVIC50:  5500   nM  BindingDB
NEVIC50:  5750   nM  BindingDB
NEVIC50:  4848   nM  BindingDB
NEVKi:  400   nM  BindingDB
NEVIC50:  80   nM  BindingDB
NEVIC50:  13000   nM  BindingDB
NEVIC50:  11800   nM  BindingDB
NEVIC50:  11300   nM  BindingDB
NEVIC50:  60   nM  BindingDB
NEVIC50:  14000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.7α = 90
b = 109.8β = 90
c = 72.9γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Database references
  • Version 1.4: 2018-01-31
    Changes: Database references
  • Version 1.5: 2018-03-14
    Changes: Database references