3ZSY

Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design

• PDB DOI: https://doi.org/10.2210/pdb3ZSY/pdb

• Classification: TRANSFERASE
• Organism(s): Human immunodeficiency virus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2011-07-01 Released: 2012-07-11 
• Deposition Author(s): Peat, T.S., Newman, J., Rhodes, D.I., Vandergraaff, N., Le, G., Jones, E.D., Smith, J.A., Coates, J.A.V., Thienthong, N., Dolezal, O., Ryan, J.H., Savage, G.P., Francis, C.L., Deadman, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.222 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

Small Molecule Inhibitors of the Ledgf Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design.

Peat, T.S., Rhodes, D.I., Vandegraaff, N., Le, G., Smith, J.A., Clark, L.J., Jones, E.D., Coates, J.A.V., Thienthong, N., Newman, J., Dolezal, O., Mulder, R., Ryan, J.H., Savage, G.P., Francis, C.L., Deadman, J.J.

(2012) PLoS One 7: 40147

• PubMed: 22808106 
• DOI: https://doi.org/10.1371/journal.pone.0040147
• Primary Citation of Related Structures:  
  3ZCM, 3ZSO, 3ZSQ, 3ZSR, 3ZSV, 3ZSW, 3ZSX, 3ZSY, 3ZSZ, 3ZT0, 3ZT1, 3ZT2, 3ZT3, 3ZT4


• PubMed Abstract: 
  

  A fragment-based screen against human immunodeficiency virus type 1 (HIV) integrase led to a number of compounds that bound to the lens epithelium derived growth factor (LEDGF) binding site of the integrase catalytic core domain. We determined the crystallographic structures of complexes of the HIV integrase catalytic core domain for 10 of these compounds and quantitated the binding by surface plasmon resonance. We demonstrate that the compounds inhibit the interaction of LEDGF with HIV integrase in a proximity AlphaScreen assay, an assay for the LEDGF enhancement of HIV integrase strand transfer and in a cell based assay. The compounds identified represent a potential framework for the development of a new series of HIV integrase inhibitors that do not bind to the catalytic site of the enzyme.

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Organizational Affiliation: 

CSIRO Materials, Science and Engineering, Parkville, Victoria, Australia. [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: 38.37 kDa 
• Atom Count: 2,564 
• Modelled Residue Count: 298 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTEGRASE	A, B	167	Human immunodeficiency virus	Mutation(s): 3  EC: 2.7.7
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OM3	G [auth A], L [auth B]	(R)-(4-CARBOXY-1,3-BENZODIOXOL-5-YL)METHYL-[[2-(CYCLOHEXYLMETHYLCARBAMOYL)PHENYL]METHYL]-METHYL-AZANIUM C25 H31 N2 O5 STKSSLWZOAVRQS-UHFFFAOYSA-O
SO4	C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	F [auth A], K [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
OM3	PDBBind:  3ZSY	Kd: 5.95e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.222 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.692	α = 90
b = 70.692	β = 90
c = 66.889	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): Peat, T.S., Newman, J., Rhodes, D.I., Vandergraaff, N., Le, G., Jones, E.D., Smith, J.A., Coates, J.A.V., Thienthong, N., Dolezal, O., Ryan, J.H., Savage, G.P., Francis, C.L., Deadman, J.J.

Revision History  

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2012-08-01
  Changes: Database references, Structure summary
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description