4KV8

Crystal structure of HIV RT in complex with BILR0355BS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.229 

wwPDB Validation   3D Report Full Report


This is version 2.1 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: https://doi.org/10.1016/j.bmcl.2013.06.007
  • Primary Citation of Related Structures:  
    4KV8

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV Reverse transcriptase P66564HIV-1 M:B_HXB2RMutation(s): 0 
Gene Names: gag-polRT
EC: 3.1.13.2
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HIV Reverse transcriptase P51442HIV-1 M:B_HXB2RMutation(s): 0 
Gene Names: gag-polRT
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1WT
Query on 1WT

Download Ideal Coordinates CCD File 
E [auth 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
MLA
Query on MLA

Download Ideal Coordinates CCD File 
D [auth A]MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
1WT Binding MOAD:  4KV8 IC50: 17 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChains NameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
C
sucroseOligosaccharide / Nutrient
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.229 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.21α = 90
b = 154.89β = 90
c = 154.29γ = 90
Software Package:
Software NamePurpose
CNXrefinement
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-08-07
    Changes: Database references
  • Version 1.2: 2015-04-29
    Changes: Non-polymer description
  • Version 1.3: 2015-05-27
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-02-28
    Changes: Data collection, Database references, Structure summary