Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 129967.02 
• Atom Count: 7894 
• Residue Count: 1120 
• Unique protein chains: 1

3LAK

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

• DOI: 10.2210/pdb3LAK/pdb

• Classification: TRANSFERASE
• Organism(s): Human immunodeficiency virus type 1 group M subtype B
• Expression System: Escherichia coli


• 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: 2.3 Å
• R-Value Free: 0.274 
• R-Value Work: 0.223 

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: 10.1016/j.bmcl.2010.01.086


• 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]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HIV Reverse transcriptase	A, B	560	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 0  Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P04585

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
KR1	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.274 
• R-Value Work: 0.223 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 118.025	α = 90.00
b = 154.603	β = 90.00
c = 154.478	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-06 
• 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
  Type: Version format compliance