6UM8 | pdb_00006um8

HIV Integrase in complex with Compound-14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 
    0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

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 Related Structures: 
    6UM8

  • 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 Early Discovery Chemistry, Bristol-Myers Squibb Research and Development, Wallingford, Connecticut 06492, United States.

Macromolecule Content 

  • Total Structure Weight: 38.99 kDa 
  • Atom Count: 2,492 
  • Modeled Residue Count: 280 
  • Deposited Residue Count: 332 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrase
A, B
166Human immunodeficiency virus 1Mutation(s): 0 
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
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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
TZXRURYHFBZSGH-MHZLTWQESA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
K [auth B],
L [auth B]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

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]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
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
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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