4KV8

Crystal structure of HIV RT in complex with BILR0355BS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

N- versus O-alkylation: Utilizing NMR methods to establish reliable primary structure determinations for drug discovery.

Laplante, S.R.Bilodeau, F.Aubry, N.Gillard, J.R.O'Meara, J.Coulombe, R.

(2013) Bioorg.Med.Chem.Lett. 23: 4663-4668

  • DOI: 10.1016/j.bmcl.2013.06.007

  • PubMed Abstract: 
  • A classic synthetic issue that remains unresolved is the reaction that involves the control of N- versus O-alkylation of ambident anions. This common chemical transformation is important for medicinal chemists, who require predictable and reliable pr ...

    A classic synthetic issue that remains unresolved is the reaction that involves the control of N- versus O-alkylation of ambident anions. This common chemical transformation is important for medicinal chemists, who require predictable and reliable protocols for the rapid synthesis of inhibitors. The uncertainty of whether the product(s) are N- and/or O-alkylated is common and can be costly if undetermined. Herein, we report an NMR-based strategy that focuses on distinguishing inhibitors and intermediates that are N- or O-alkylated. The NMR strategy involves three independent and complementary methods. However, any combination of two of the methods can be reliable if the third were compromised due to resonance overlap or other issues. The timely nature of these methods (HSQC/HMQC, HMBC. ROESY, and (13)C shift predictions) allows for contemporaneous determination of regioselective alkylation as needed during the optimization of synthetic routes.


    Organizational Affiliation

    Department of Chemistry, Boehringer Ingelheim (Canada) Ltd, 2100 Cunard St., Laval, Quebec H7S 2G5, Canada. stevenrlaplante@gmail.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV Reverse transcriptase P66
A
564Human 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
HIV Reverse transcriptase P51
B
442Human 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
B
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
1WT
Query on 1WT

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Download CCD File 
A
11-ethyl-5-methyl-8-[2-(1-oxidanylquinolin-4-yl)oxyethyl]dipyrido[3,2-[1,4]diazepin-6-one
C25 H24 N5 O3
PQGWYSJEHPHRGI-UHFFFAOYSA-N
 Ligand Interaction
MLA
Query on MLA

Download SDF File 
Download CCD File 
A
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1WTIC50: 17 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.229 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 117.210α = 90.00
b = 154.890β = 90.00
c = 154.290γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement
CNXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-05-22 
  • Released Date: 2013-07-31 
  • Deposition Author(s): Coulombe, R.

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-08-07
    Type: Database references
  • Version 1.2: 2015-04-29
    Type: Non-polymer description
  • Version 1.3: 2015-05-27
    Type: Other