3LAK | pdb_00003lak

Crystal structure of HIV-1 reverse transcriptase in complex with N1-heterocycle pyrimidinedione non-nucleoside inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3LAK/pdb

• Classification: TRANSFERASE
• Organism(s): HIV-1 M:B_HXB2R
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-06 Released: 2010-02-23 
• Deposition Author(s): Lansdon, E.B., Mitchell, M.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.274 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

N1-Heterocyclic pyrimidinediones as non-nucleoside inhibitors of HIV-1 reverse transcriptase.

Mitchell, M.L., Son, J.C., Lee, I.Y., Lee, C.K., Kim, H.S., Guo, H., Wang, J., Hayes, J., Wang, M., Paul, A., Lansdon, E.B., Chen, J.M., Eisenberg, G., Geleziunas, R., Xu, L., Kim, C.U.

(2010) Bioorg Med Chem Lett 20: 1585-1588

• PubMed: 20137928 
• DOI: https://doi.org/10.1016/j.bmcl.2010.01.086
• Primary Citation Related Structures: 
  3LAK


• PubMed Abstract: 
  

  A series of N1-heterocyclic pyrimidinediones were extensively evaluated as HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs). Inhibitor 1 is active against NNRTI-resistant viruses including RT mutant K103N. The co-crystal structure of inhibitor 1 with HIV-1 RT revealed that H-bonds are formed with K101 and K103. Efforts to improve the suboptimal pharmacokinetic profile of 1 resulted in the discovery of compound 13, which represents the lead compound in this series with improved pharmacokinetics and similar potency as inhibitor 1.

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Organizational Affiliation: 
• Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 129.97 kDa 
• Atom Count: 8,101 
• Modeled Residue Count: 956 
• Deposited Residue Count: 1,120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV Reverse transcriptase	A, B	560	HIV-1 M:B_HXB2R	Mutation(s): 0  EC: 2.7.7.49
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KR1	C [auth A]	3-({3-[(2-amino-6-fluoropyridin-4-yl)methyl]-5-(1-methylethyl)-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl}carbonyl)-5-methylbenzonitrile C22 H20 F N5 O3 SORPAQIMHXALKW-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.274 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.025	α = 90
b = 154.603	β = 90
c = 154.478	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
EPMR	phasing
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Lansdon, E.B., Mitchell, M.L.

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description