3MEC

HIV-1 Reverse Transcriptase in Complex with TMC125

• PDB DOI: https://doi.org/10.2210/pdb3MEC/pdb

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


• Deposited: 2010-03-31 Released: 2010-05-12 
• Deposition Author(s): Lansdon, E.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.270 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 

Starting Model: experimental

Literature

Crystal Structures of HIV-1 Reverse Transcriptase with Etravirine (TMC125) and Rilpivirine (TMC278): Implications for Drug Design.

Lansdon, E.B., Brendza, K.M., Hung, M., Wang, R., Mukund, S., Jin, D., Birkus, G., Kutty, N., Liu, X.

(2010) J Med Chem 53: 4295-4299

• PubMed: 20438081 
• DOI: https://doi.org/10.1021/jm1002233
• Primary Citation of Related Structures:  
  3MEC, 3MED, 3MEE, 3MEG


• PubMed Abstract: 
  

  Diarylpyrimidine (DAPY) non-nucleoside reverse transcriptase inhibitors (NNRTIs) have inherent flexibility, helping to maintain activity against a wide range of resistance mutations. Crystal structures were determined with wild-type and K103N HIV-1 reverse transcriptase with etravirine (TMC125) and rilpivirine (TMC278). These structures reveal a similar binding mode for TMC125 and TMC278, whether bound to wild-type or K103N RT. Comparison to previously published structures reveals differences in binding modes for TMC125 and differences in protein conformation for TMC278.

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Organizational Affiliation: 

Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 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: 116.88 kDa 
• Atom Count: 8,072 
• Modelled Residue Count: 951 
• Deposited Residue Count: 1,000 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
p66 Reverse transcriptase	A	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
p51 Reverse transcriptase	B	440	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
65B	C [auth A]	4-({6-AMINO-5-BROMO-2-[(4-CYANOPHENYL)AMINO]PYRIMIDIN-4-YL}OXY)-3,5-DIMETHYLBENZONITRILE C20 H15 Br N6 O PYGWGZALEOIKDF-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: 2.30 Å
• R-Value Free: 0.270 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.947	α = 90
b = 154.122	β = 90
c = 154.769	γ = 90

Software Package:

Software Name	Purpose
BOX	data collection
AMoRE	phasing
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Lansdon, E.B.

Revision History  

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-07-18
  Changes: Non-polymer description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description