4I7F

HIV-1 Reverse Transcriptase in complex with a phosphonate analog of nevirapine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthesis and biological evaluation of phosphonate analogues of nevirapine.

Parrish, J.Tong, L.Wang, M.Chen, X.Lansdon, E.B.Cannizzaro, C.Zheng, X.Desai, M.C.Xu, L.

(2013) Bioorg.Med.Chem.Lett. 23: 1493-1497

  • DOI: 10.1016/j.bmcl.2012.12.049

  • PubMed Abstract: 
  • A series of nevirapine-based analogues containing the phosphonate functionality were prepared and evaluated in vitro against HIV RT. The effect of the phosphonate was evaluated against the wild type and Y181C HIV replication. An in vivo PK study was ...

    A series of nevirapine-based analogues containing the phosphonate functionality were prepared and evaluated in vitro against HIV RT. The effect of the phosphonate was evaluated against the wild type and Y181C HIV replication. An in vivo PK study was performed on a select analogue.


    Organizational Affiliation

    Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA. Jay.Parrish@gilead.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase
A
560Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase
B
440Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NVE
Query on NVE

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A
diethyl ({4-[2-(11-ethyl-5-methyl-6-oxo-6,11-dihydro-5H-dipyrido[3,2-b:2',3'-e][1,4]diazepin-8-yl)ethyl]phenoxy}methyl)phosphonate
nevirapine phosphonate analogue
C27 H33 N4 O5 P
YVBXNGRTCURFDW-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NVEIC50: 100 nM BINDINGMOAD
NVEIC50: 100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.221 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 118.319α = 90.00
b = 154.703β = 90.00
c = 154.250γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
BOSdata collection
EPMRphasing
HKL-2000data scaling
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-03-06
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description