8CTA

Minimal 2:2 Ternary Complex between BI-224436 bound HIV-1 Integrase Catalytic Core Domain Dimer and Carboxy Terminal Domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 angstrom resolution: Routes to inhibitor optimization.

Eilers, G.Gupta, K.Allen, A.Montermoso, S.Murali, H.Sharp, R.Hwang, Y.Bushman, F.D.Van Duyne, G.

(2023) PLoS Pathog 19: e1011097-e1011097

  • DOI: https://doi.org/10.1371/journal.ppat.1011097
  • Primary Citation of Related Structures:  
    8CT5, 8CT7, 8CTA

  • PubMed Abstract: 

    HIV integrase (IN) inserts viral DNA into the host genome and is the target of the strand transfer inhibitors (STIs), a class of small molecules currently in clinical use. Another potent class of antivirals is the allosteric inhibitors of integrase, or ALLINIs. ALLINIs promote IN aggregation by stabilizing an interaction between the catalytic core domain (CCD) and carboxy-terminal domain (CTD) that undermines viral particle formation in late replication. Ongoing challenges with inhibitor potency, toxicity, and viral resistance motivate research to understand their mechanism. Here, we report a 2.93 Å X-ray crystal structure of the minimal ternary complex between CCD, CTD, and the ALLINI BI-224436. This structure reveals an asymmetric ternary complex with a prominent network of π-mediated interactions that suggest specific avenues for future ALLINI development and optimization.


  • Organizational Affiliation

    Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrase
A, B, E, F, I
A, B, E, F, I, J, M, N
161Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: pol
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Integrase
C, D, G, H, K
C, D, G, H, K, L, O, P
53Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: pol
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L3D (Subject of Investigation/LOI)
Query on L3D

Download Ideal Coordinates CCD File 
CA [auth F]
JA [auth I]
LA [auth J]
Q [auth A]
S [auth B]
CA [auth F],
JA [auth I],
LA [auth J],
Q [auth A],
S [auth B],
SA [auth M],
UA [auth N],
X [auth E]
(2S)-tert-butoxy[4-(2,3-dihydropyrano[4,3,2-de]quinolin-7-yl)-2-methylquinolin-3-yl]acetic acid
C27 H26 N2 O4
MIXIIJCBELCMCZ-VWLOTQADSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth F]
DA [auth F]
EA [auth F]
FA [auth F]
AA [auth E],
BA [auth F],
DA [auth F],
EA [auth F],
FA [auth F],
GA [auth F],
HA [auth G],
IA [auth H],
KA [auth I],
MA [auth J],
NA [auth K],
OA [auth K],
PA [auth L],
QA [auth L],
R [auth A],
RA [auth L],
T [auth B],
TA [auth M],
U [auth B],
V [auth D],
VA [auth N],
W [auth D],
WA [auth N],
XA [auth O],
Y [auth E],
YA [auth P],
Z [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.51α = 90
b = 116.51β = 103.61
c = 112.8γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 AI 052845

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description