4TSX

HIV-1 Integrase Catalytic Core Domain Mutant Complexed with Allosteric Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The mechanism of H171T resistance reveals the importance of N -protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase.

Slaughter, A.Jurado, K.A.Deng, N.Feng, L.Kessl, J.J.Shkriabai, N.Larue, R.C.Fadel, H.J.Patel, P.A.Jena, N.Fuchs, J.R.Poeschla, E.Levy, R.M.Engelman, A.Kvaratskhelia, M.

(2014) Retrovirology 11: 100-100

  • DOI: 10.1186/s12977-014-0100-1
  • Primary Citation of Related Structures:  
    4TSX

  • PubMed Abstract: 
  • Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are an important new class of anti-HIV-1 agents. ALLINIs bind at the IN catalytic core domain (CCD) dimer interface occupying the principal binding pocket of its cellular cofactor LEDGF/p75. Consequently, ALLINIs inhibit HIV-1 IN interaction with LEDGF/p75 as well as promote aberrant IN multimerization ...

    Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are an important new class of anti-HIV-1 agents. ALLINIs bind at the IN catalytic core domain (CCD) dimer interface occupying the principal binding pocket of its cellular cofactor LEDGF/p75. Consequently, ALLINIs inhibit HIV-1 IN interaction with LEDGF/p75 as well as promote aberrant IN multimerization. Selection of viral strains emerging under the inhibitor pressure has revealed mutations at the IN dimer interface near the inhibitor binding site.


    Organizational Affiliation

    Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 496 W. 12th Ave, 508 Riffe Building, Columbus, OH, 43210, USA. kvaratskhelia.1@osu.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IntegraseA163Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: pol
UniProt
Find proteins for F2WR39 (Human immunodeficiency virus 1)
Explore F2WR39 
Go to UniProtKB:  F2WR39
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LF0 (Subject of Investigation/LOI)
Query on LF0

Download Ideal Coordinates CCD File 
B [auth A](2S)-tert-butoxy[4-(3,4-dihydro-2H-chromen-6-yl)-2-methylquinolin-3-yl]ethanoic acid
C25 H27 N O4
ZFERZAMPQIXCPM-QHCPKHFHSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAF
Query on CAF
AL-PEPTIDE LINKINGC5 H12 As N O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
LF0 BindingDB:  4TSX Kd: 24 (nM) from 1 assay(s)
Binding MOAD:  4TSX Kd: 1.03e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.248α = 90
b = 72.248β = 90
c = 66.032γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description, Source and taxonomy