HIV Integrase in complex with Compound-14

Experimental Data Snapshot

  • Resolution: 2.33 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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Discovery and Optimization of Novel Pyrazolopyrimidines as Potent and Orally Bioavailable Allosteric HIV-1 Integrase Inhibitors.

Li, G.Meanwell, N.A.Krystal, M.R.Langley, D.R.Naidu, B.N.Sivaprakasam, P.Lewis, H.Kish, K.Khan, J.A.Ng, A.Trainor, G.L.Cianci, C.Dicker, I.B.Walker, M.A.Lin, Z.Protack, T.Discotto, L.Jenkins, S.Gerritz, S.W.Pendri, A.

(2020) J Med Chem 63: 2620-2637

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01681
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The standard of care for HIV-1 infection, highly active antiretroviral therapy (HAART), combines two or more drugs from at least two classes. Even with the success of HAART, new drugs with novel mechanisms are needed to combat viral resistance, improve adherence, and mitigate toxicities. Active site inhibitors of HIV-1 integrase are clinically validated for the treatment of HIV-1 infection. Here we describe allosteric inhibitors of HIV-1 integrase that bind to the LEDGF/p75 interaction site and disrupt the structure of the integrase multimer that is required for the HIV-1 maturation. A series of pyrazolopyrimidine-based inhibitors was developed with a vector in the 2-position that was optimized by structure-guided compound design. This resulted in the discovery of pyrazolopyrimidine 3 , which was optimized at the 2- and 7-positions to afford 26 and 29 as potent allosteric inhibitors of HIV-1 integrase that exhibited low nanomolar antiviral potency in cell culture and encouraging PK properties.

  • Organizational Affiliation

    Department of Molecular Structure and Design, Bristol-Myers Squibb Research and Development, Princeton, New Jersey 08543-4000, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
166Human immunodeficiency virus 1Mutation(s): 0 
EC: (UniProt), (UniProt), (UniProt), (UniProt), (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QCG (Subject of Investigation/LOI)
Query on QCG

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B]
(2S)-tert-butoxy[7-(8-fluoro-5-methyl-3,4-dihydro-2H-1-benzopyran-6-yl)-5-methyl-2-phenylpyrazolo[1,5-a]pyrimidin-6-yl]acetic acid
C29 H30 F N3 O4
Query on 1PE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
K [auth B],
L [auth B]
C10 H22 O6
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
C4 H10 O3
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
N [auth B]
O [auth B]
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B]
O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
QCG Binding MOAD:  6UM8 Ki: 170 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.33 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.626α = 90
b = 164.626β = 90
c = 164.626γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description