HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor STP0404 (Pirmitegravir)

Experimental Data Snapshot

  • Resolution: 2.06 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


The Drug-Induced Interface That Drives HIV-1 Integrase Hypermultimerization and Loss of Function.

Singer, M.R.Dinh, T.Levintov, L.Annamalai, A.S.Rey, J.S.Briganti, L.Cook, N.J.Pye, V.E.Taylor, I.A.Kim, K.Engelman, A.N.Kim, B.Perilla, J.R.Kvaratskhelia, M.Cherepanov, P.

(2023) mBio 14: e0356022-e0356022

  • DOI: https://doi.org/10.1128/mbio.03560-22
  • Primary Citation of Related Structures:  
    8A1P, 8A1Q

  • PubMed Abstract: 

    Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are an emerging class of small molecules that disrupt viral maturation by inducing the aberrant multimerization of IN. Here, we present cocrystal structures of HIV-1 IN with two potent ALLINIs, namely, BI-D and the drug candidate Pirmitegravir. The structures reveal atomistic details of the ALLINI-induced interface between the HIV-1 IN catalytic core and carboxyl-terminal domains (CCD and CTD). Projecting from their principal binding pocket on the IN CCD dimer, the compounds act as molecular glue by engaging a triad of invariant HIV-1 IN CTD residues, namely, Tyr226, Trp235, and Lys266, to nucleate the CTD-CCD interaction. The drug-induced interface involves the CTD SH3-like fold and extends to the beginning of the IN carboxyl-terminal tail region. We show that mutations of HIV-1 IN CTD residues that participate in the interface with the CCD greatly reduce the IN-aggregation properties of Pirmitegravir. Our results explain the mechanism of the ALLINI-induced condensation of HIV-1 IN and provide a reliable template for the rational development of this series of antiretrovirals through the optimization of their key contacts with the viral target. IMPORTANCE Despite the remarkable success of combination antiretroviral therapy, HIV-1 remains among the major causes of human suffering and loss of life in poor and developing nations. To prevail in this drawn-out battle with the pandemic, it is essential to continue developing advanced antiviral agents to fight drug resistant HIV-1 variants. Allosteric integrase inhibitors (ALLINIs) are an emerging class of HIV-1 antagonists that are orthogonal to the current antiretroviral drugs. These small molecules act as highly specific molecular glue, which triggers the aggregation of HIV-1 integrase. In this work, we present high-resolution crystal structures that reveal the crucial interactions made by two potent ALLINIs, namely, BI-D and Pirmitegravir, with HIV-1 integrase. Our results explain the mechanism of drug action and will inform the development of this promising class of small molecules for future use in antiretroviral regimens.

  • Organizational Affiliation

    Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
233Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: gag-pol
EC: 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WBV (Subject of Investigation/LOI)
Query on WBV

Download Ideal Coordinates CCD File 
N [auth B],
R [auth D]
(2S)-tert-butoxy{4-(4-chlorophenyl)-2,3,6-trimethyl-1-[(1-methyl-1H-pyrazol-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-5-yl}acetic acid
C27 H31 Cl N4 O3
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth B]
H [auth B]
I [auth B]
E [auth A],
F [auth A],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
P [auth C],
Q [auth C],
S [auth D],
T [auth D],
U [auth D],
V [auth D]
C2 H6 O2
Query on MG

Download Ideal Coordinates CCD File 
O [auth B],
W [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.06 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.262α = 90
b = 69.258β = 102.38
c = 64.106γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
DIALSdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomFC001061
Medical Research Council (MRC, United Kingdom)United KingdomFC001061
Wellcome TrustUnited KingdomFC001061
The Francis Crick InstituteUnited KingdomFC001061

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-03-15
    Changes: Database references
  • Version 1.3: 2023-03-22
    Changes: Database references
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Source and taxonomy, Structure summary