2YNG | pdb_00002yng

HIV-1 Reverse Transcriptase in complex with inhibitor GSK560

• PDB DOI: https://doi.org/10.2210/pdb2YNG/pdb

• Classification: HYDROLASE
• Organism(s): HIV-1 M:B_HXB2R
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-10-14 Released: 2013-01-09 
• Deposition Author(s): Chong, P., Sebahar, P., Youngman, M., Garrido, D., Zhang, H., Stewart, E.L., Nolte, R.T., Wang, L., Ferris, R.G., Edelstein, M., Weaver, K., Mathis, A., Peat, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Rational Design of Potent Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase.

Chong, P., Sebahar, P., Youngman, M., Garrido, D., Zhang, H., Stewart, E.L., Nolte, R.T., Wang, L., Ferris, R.G., Edelstein, M., Weaver, K., Mathis, A., Peat, A.

(2012) J Med Chem 55: 10601

• PubMed: 23137340 
• DOI: https://doi.org/10.1021/jm301294g
• Primary Citation of Related Structures:  
  2YNF, 2YNG, 2YNH, 2YNI


• PubMed Abstract: 
  

  A new series of non-nucleoside reverse transcriptase inhibitors based on an imidazole-amide biarylether scaffold has been identified and shown to possess potent antiviral activity against HIV-1, including the NNRTI-resistant Y188L mutated virus. X-ray crystallography of inhibitors bound to reverse transcriptase, including a structure of the Y188L RT protein, was used extensively to help identify and optimize the key hydrogen-bonding motif. This led directly to the design of compound 43 that exhibits remarkable antiviral activity (EC50<1 nM) against a wide range of NNRTI-resistant viruses and a favorable pharmacokinetic profile across multiple species.

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Organizational Affiliation: 

GlaxoSmithKline Research & Development, 5 Moore Drive, Research Triangle Park, North Carolina 27709, United States.

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: 117.86 kDa 
• Atom Count: 8,582 
• Modelled Residue Count: 971 
• Deposited Residue Count: 1,010 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REVERSE TRANSCRIPTASE/RIBONUCLEASE H	A	563	HIV-1 M:B_HXB2R	Mutation(s): 0  EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.1.13.2 (PDB Primary Data)
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P51 RT	B	447	HIV-1 M:B_HXB2R	Mutation(s): 0
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
WHU	G [auth A]	2-azanyl-N-[[4-bromanyl-3-(3-chloranyl-5-cyano-phenoxy)-2-fluoranyl-phenyl]methyl]-4-chloranyl-1H-imidazole-5-carboxamide C18 H11 Br Cl2 F N5 O2 IZRLYEGHBQTAFO-UHFFFAOYSA-N
SRT	F [auth A]	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.876	α = 90
b = 154.627	β = 90
c = 156.958	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-09 
Deposition Author(s): Chong, P., Sebahar, P., Youngman, M., Garrido, D., Zhang, H., Stewart, E.L., Nolte, R.T., Wang, L., Ferris, R.G., Edelstein, M., Weaver, K., Mathis, A., Peat, A.

Revision History  

• Version 1.0: 2013-01-09
  Type: Initial release
  
• Version 1.1: 2013-12-18
  Changes: Structure summary
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description