3LAL

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

• PDB DOI: https://doi.org/10.2210/pdb3LAL/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: 2.51 Å
• R-Value Free: 
  0.267 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

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

Mitchell, M.L., Son, J.C., Guo, H., Im, Y.A., Cho, E.J., Wang, J., Hayes, J., Wang, M., Paul, A., Lansdon, E.B., Chen, J.M., Graupe, D., Rhodes, G., He, G.X., Geleziunas, R., Xu, L., Kim, C.U.

(2010) Bioorg Med Chem Lett 20: 1589-1592

• PubMed: 20138513 
• DOI: https://doi.org/10.1016/j.bmcl.2010.01.085
• Primary Citation of Related Structures:  
  3LAL, 3LAM, 3LAN


• PubMed Abstract: 
  

  A series of N1-alkyl pyrimidinediones were designed, synthesized and evaluated as HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs). Our efforts identified compound 10b, which represents the lead compound in this series with pharmacokinetics and antiviral potency that may support once-daily dosing.

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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: 129.93 kDa 
• Atom Count: 8,013 
• Modelled 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KRV	C [auth A]	3-{[3-ethyl-5-(1-methylethyl)-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl]carbonyl}-5-methylbenzonitrile C18 H19 N3 O3 AYPIJAMXGVYYRQ-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.267 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.151	α = 90
b = 154.124	β = 90
c = 153.956	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