Core Catalytic Domain of HIV Integrase in complex with virtual screening hit

Experimental Data Snapshot

  • Resolution: 2.32 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report

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Augmenting Hit Identification by Virtual Screening Techniques in Small Molecule Drug Discovery.

Yan, X.C.Sanders, J.M.Gao, Y.D.Tudor, M.Haidle, A.M.Klein, D.J.Converso, A.Lesburg, C.A.Zang, Y.Wood, H.B.

(2020) J Chem Inf Model 60: 4144-4152

  • DOI: https://doi.org/10.1021/acs.jcim.0c00113
  • Primary Citation of Related Structures:  
    6VLM, 6VLU, 6VLV

  • PubMed Abstract: 

    Two orthogonal approaches for hit identification in drug discovery are large-scale in vitro and in silico screening. In recent years, due to the emergence of new targets and a rapid increase in the size of the readily synthesizable chemical space, there is a growing emphasis on the integration of the two techniques to improve the hit finding efficiency. Here, we highlight three examples of drug discovery projects at Merck & Co., Inc., Kenilworth, NJ, USA in which different virtual screening (VS) techniques, each specifically tailored to leverage knowledge available for the target, were utilized to augment the selection of high-quality chemical matter for in vitro assays and to enhance the diversity and tractability of hits. Central to success is a fully integrated workflow combining in silico and experimental expertise at every stage of the hit identification process. We advocate that workflows encompassing VS as part of an integrated hit finding plan should be widely adopted to accelerate hit identification and foster cross-functional collaborations in modern drug discovery.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
177Human immunodeficiency virus 1Mutation(s): 0 
EC: (UniProt), (UniProt), (UniProt), (UniProt), (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03367 
Go to UniProtKB:  P03367
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03367
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R2D (Subject of Investigation/LOI)
Query on R2D

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B],
E [auth B]
[3-(4-chlorophenyl)[1,3]thiazolo[3,2-a]benzimidazol-2-yl]acetic acid
C17 H11 Cl N2 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
R2D Binding MOAD:  6VLM IC50: 1.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.32 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.9α = 90
b = 66.77β = 102.33
c = 57.43γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
autoPROCdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references, Refinement description