7SNL

Disulfide stabilized HIV-1 CA hexamer in complex with capsid inhibitor N-(1-(3-(4-chloro-1-methyl-3-(methylsulfonamido)-1H-indazol-7-yl)-4-oxo-3,4-dihydropyrido[2,3-d]pyrimidin-2-yl)-2-(3,5-difluorophenyl)ethyl)-2-(3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl)acetamide

• PDB DOI: https://doi.org/10.2210/pdb7SNL/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus type 1 BH10
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-10-28 Released: 2022-10-05 
• Deposition Author(s): Bester, S.M., Kvaratskhelia, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.261 
• R-Value Work: 0.243 
• R-Value Observed: 0.244 

Literature

Disulfide stabilized HIV-1 CA hexamer in complex with capsid inhibitor N-(1-(3-(4-chloro-1-methyl-3-(methylsulfonamido)-1H-indazol-7-yl)-4-oxo-3,4-dihydropyrido[2,3-d]pyrimidin-2-yl)-2-(3,5-difluorophenyl)ethyl)-2-(3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl)acetamide

Adu-Ampratwum, D., Haney, R., Bester, S.M., Annamalai, A.S., Wei, G., Fuchs, J.R., Kvaratskhelia, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 27.01 kDa 
• Atom Count: 1,801 
• Modelled Residue Count: 210 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein p24	A	231	Human immunodeficiency virus type 1 BH10	Mutation(s): 4  Gene Names: gag-pol
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9VI (Subject of Investigation/LOI)	B [auth A]	N-[(1S)-1-(3-{4-chloro-3-[(methanesulfonyl)amino]-1-methyl-1H-indazol-7-yl}-4-oxo-3,4-dihydropyrido[2,3-d]pyrimidin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[3-(trifluoromethyl)-6,7-dihydro-1H-indazol-1-yl]acetamide C34 H27 Cl F5 N9 O4 S ZBYBMYJJANJYNU-QHCPKHFHSA-N
IOD	C [auth A], D [auth A], E [auth A], F [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
CL	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.261 
• R-Value Work: 0.243 
• R-Value Observed: 0.244 
• Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.26	α = 90
b = 92.26	β = 90
c = 57.98	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-05 
Deposition Author(s): Bester, S.M., Kvaratskhelia, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI157802
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U54-AI150472

Revision History  

• Version 1.0: 2022-10-05
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description