4E1M | pdb_00004e1m

Crystal Structure of HIV-1 Integrase with a non-catayltic site inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4E1M/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-03-06 Released: 2012-04-25 
• Deposition Author(s): Lansdon, E.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.273 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

New Class of HIV-1 Integrase (IN) Inhibitors with a Dual Mode of Action.

Tsiang, M., Jones, G.S., Niedziela-Majka, A., Kan, E., Lansdon, E.B., Huang, W., Hung, M., Samuel, D., Novikov, N., Xu, Y., Mitchell, M., Guo, H., Babaoglu, K., Liu, X., Geleziunas, R., Sakowicz, R.

(2012) J Biological Chem 287: 21189-21203

• PubMed: 22535962 
• DOI: https://doi.org/10.1074/jbc.M112.347534
• Primary Citation Related Structures: 
  4E1M, 4E1N


• PubMed Abstract: 
  

  tert-Butoxy-(4-phenyl-quinolin-3-yl)-acetic acids (tBPQA) are a new class of HIV-1 integrase (IN) inhibitors that are structurally distinct from IN strand transfer inhibitors but analogous to LEDGINs. LEDGINs are a class of potent antiviral compounds that interacts with the lens epithelium-derived growth factor (LEDGF) binding pocket on IN and were identified through competition binding against LEDGF. LEDGF tethers IN to the host chromatin and enables targeted integration of viral DNA. The prevailing understanding of the antiviral mechanism of LEDGINs is that they inhibit LEDGF binding to IN, which prevents targeted integration of HIV-1. We showed that in addition to the properties already known for LEDGINs, the binding of tBPQAs to the IN dimer interface inhibits IN enzymatic activity in a LEDGF-independent manner. Using the analysis of two long terminal repeat junctions in HIV-infected cells, we showed that the inhibition by tBPQAs occurs at or prior to the viral DNA 3'-processing step. Biochemical studies revealed that this inhibition operates by compound-induced conformational changes in the IN dimer that prevent proper assembly of IN onto viral DNA. For the first time, tBPQAs were demonstrated to be allosteric inhibitors of HIV-1 IN displaying a dual mode of action: inhibition of IN-viral DNA assembly and inhibition of IN-LEDGF interaction.

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Organizational Affiliation: 
• Gilead Sciences, Inc, Foster City, California 94404, USA. [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: 18.78 kDa 
• Atom Count: 1,217 
• Modeled Residue Count: 148 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Integrase	A	166	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	Mutation(s): 1
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TQ2	B [auth A]	(2S)-tert-butoxy[4-(3,4-dimethylphenyl)-2-methylquinolin-3-yl]ethanoic acid C24 H27 N O3 HGSMBBVZYWHGQB-QFIPXVFZSA-N

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: 1.90 Å
• R-Value Free:  0.273 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.794	α = 90
b = 71.794	β = 90
c = 65.329	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Lansdon, E.B.

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2012-05-09
  Changes: Database references
• Version 1.2: 2012-07-25
  Changes: Database references
• Version 1.3: 2020-02-26
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary