5KGX | pdb_00005kgx

HIV1 catalytic core domain in complex with an inhibitor (2~{S})-2-[3-(3,4-dihydro-2~{H}-chromen-6-yl)-1-methyl-indol-2-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid

• PDB DOI: https://doi.org/10.2210/pdb5KGX/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-06-13 Released: 2016-10-19 
• Deposition Author(s): Feng, L., Kobe, M., Kvaratskhelia, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 
  0.244 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.198 (DCC) 

Literature

Indole-based allosteric inhibitors of HIV-1 integrase.

Patel, P.A., Kvaratskhelia, N., Mansour, Y., Antwi, J., Feng, L., Koneru, P., Kobe, M.J., Jena, N., Shi, G., Mohamed, M.S., Li, C., Kessl, J.J., Fuchs, J.R.

(2016) Bioorg Med Chem Lett 26: 4748-4752

• PubMed: 27568085 
• DOI: https://doi.org/10.1016/j.bmcl.2016.08.037
• Primary Citation Related Structures: 
  5KGW, 5KGX


• PubMed Abstract: 
  

  Employing a scaffold hopping approach, a series of allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) have been synthesized based on an indole scaffold. These compounds incorporate the key elements utilized in quinoline-based ALLINIs for binding to the IN dimer interface at the principal LEDGF/p75 binding pocket. The most potent of these compounds displayed good activity in the LEDGF/p75 dependent integration assay (IC50=4.5μM) and, as predicted based on the geometry of the five- versus six-membered ring, retained activity against the A128T IN mutant that confers resistance to many quinoline-based ALLINIs.

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Organizational Affiliation: 
• Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Department of Chemistry, The Ohio State University, Columbus, OH 43210, United States.
Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States.
Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt.
Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States.
Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt.
Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States. Electronic address: [e-mail].
Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.67 kDa 
• Atom Count: 1,112 
• Modeled Residue Count: 136 
• Deposited Residue Count: 163 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A	163	Human immunodeficiency virus 1	Mutation(s): 2
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7SK	B [auth A]	(2S)-tert-butoxy[3-(3,4-dihydro-2H-1-benzopyran-6-yl)-1-methyl-1H-indol-2-yl]acetic acid C24 H27 N O4 JEETZBQOULTRJG-QFIPXVFZSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF	A	L-PEPTIDE LINKING	C5 H12 As N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free:  0.244 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.198 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.109	α = 90
b = 72.109	β = 90
c = 65.713	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-19 
Deposition Author(s): Feng, L., Kobe, M., Kvaratskhelia, M.

Revision History  

• Version 1.0: 2016-10-19
  Type: Initial release
  
• Version 1.1: 2016-11-02
  Changes: Non-polymer description
• Version 1.2: 2018-03-07
  Changes: Data collection, Derived calculations
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary