1IKV

K103N Mutant HIV-1 Reverse Transcriptase in Complex with Efivarenz


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural basis for the inhibitory efficacy of efavirenz (DMP-266), MSC194 and PNU142721 towards the HIV-1 RT K103N mutant.

Lindberg, J.Sigurdsson, S.Lowgren, S.Andersson, H.O.Sahlberg, C.Noreen, R.Fridborg, K.Zhang, H.Unge, T.

(2002) Eur J Biochem 269: 1670-1677

  • DOI: 10.1046/j.1432-1327.2002.02811.x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The K103N substitution is a frequently observed HIV-1 RT mutation in patients who do not respond to combination-therapy. The drugs Efavirenz, MSC194 and PNU142721 belong to the recent generation of NNRTIs characterized by an improved resistance profi ...

    The K103N substitution is a frequently observed HIV-1 RT mutation in patients who do not respond to combination-therapy. The drugs Efavirenz, MSC194 and PNU142721 belong to the recent generation of NNRTIs characterized by an improved resistance profile to the most common single point mutations within HIV-1 RT, including the K103N mutation. In the present study we present structural observations from Efavirenz in complex with wild-type protein and the K103N mutant and PNU142721 and MSC194 in complex with the K103N mutant. The structures unanimously indicate that the K103N substitution induces only minor positional adjustments of the three inhibitors and the residues lining the binding pocket. Thus, compared to the corresponding wild-type structures, these inhibitors bind to the mutant in a conservative mode rather than through major rearrangements. The structures implicate that the reduced inhibitory efficacy should be attributed to the changes in the chemical environment in the vicinity of the substituted N103 residue. This is supported by changes in hydrophobic and electrostatic interactions to the inhibitors between wild-type and K103N mutant complexes. These potent inhibitors accommodate to the K103N mutation by forming new interactions to the N103 side chain. Our results are consistent with the proposal by Hsiou et al. [Hsiou, Y., Ding, J., Das, K., Clark, A.D. Jr, Boyer, P.L., Lewi, P., Janssen, P.A., Kleim, J.P., Rosner, M., Hughes, S.H. & Arnold, E. (2001) J. Mol. Biol. 309, 437-445] that inhibitors with good activity against the K103N mutant would be expected to have favorable interactions with the mutant asparagines side chain, thereby compensating for resistance caused by stabilization of the mutant enzyme due to a hydrogen-bond network involving the N103 and Y188 side chains.


    Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala Biomedical Center, Uppsala University, Sweden.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POL POLYPROTEIN
A
560Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: BH10
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 P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
POL POLYPROTEIN
B
427Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: BH10
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 P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EFZ
Query on EFZ

Download CCD File 
A
(-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE
C14 H9 Cl F3 N O2
XPOQHMRABVBWPR-ZDUSSCGKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EFZEC50:  57   nM  BindingDB
EFZKi:  380   nM  BindingDB
EFZKi:  25   nM  BindingDB
EFZIC50:  20   nM  BindingDB
EFZIC50:  21   nM  BindingDB
EFZKi:  30   nM  BindingDB
EFZIC50:  364   nM  BindingDB
EFZIC50:  25   nM  BindingDB
EFZEC50:  4   nM  BindingDB
EFZKi:  40   nM  BindingDB
EFZIC50 :  520   nM  PDBBind
EFZIC50:  2100   nM  BindingDB
EFZIC50:  6.900000095367432   nM  BindingDB
EFZIC50:  9.5   nM  BindingDB
EFZIC50:  0.75   nM  BindingDB
EFZIC50:  3400   nM  BindingDB
EFZKi:  17   nM  BindingDB
EFZIC50:  14   nM  BindingDB
EFZKi:  300   nM  BindingDB
EFZIC50:  61   nM  BindingDB
EFZIC50:  0.800000011920929   nM  BindingDB
EFZIC50:  4   nM  BindingDB
EFZKi:  100   nM  BindingDB
EFZEC50:  200   nM  BindingDB
EFZIC50:  85   nM  BindingDB
EFZKi:  120   nM  BindingDB
EFZIC50:  6   nM  BindingDB
EFZEC50:  1   nM  BindingDB
EFZKi:  160   nM  BindingDB
EFZKi:  150   nM  BindingDB
EFZEC50:  300   nM  BindingDB
EFZIC50:  500   nM  BindingDB
EFZKi:  3   nM  BindingDB
EFZIC50:  33   nM  BindingDB
EFZIC50:  38   nM  BindingDB
EFZIC50:  40   nM  BindingDB
EFZIC50:  20   nM  BindingDB
EFZIC50:  47   nM  BindingDB
EFZIC50:  48   nM  BindingDB
EFZIC50:  800   nM  BindingDB
EFZIC50:  54   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.228 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.633α = 90
b = 157.168β = 90
c = 156.149γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2001-05-07 
  • Released Date: 2001-06-06 
  • Deposition Author(s): Lindberg, J., Unge, T.

Revision History 

  • Version 1.0: 2001-06-06
    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: 2011-08-31
    Changes: Atomic model
  • Version 1.4: 2012-07-18
    Changes: Non-polymer description
  • Version 1.5: 2018-03-07
    Changes: Advisory, Data collection