Roles of Conformational and Positional Adaptability in Structure-Based Design of TMC125-R165335 (Etravirine) and Related Non-nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent and Effective against Wild-Type and Drug-Resistant HIV-1 Variants.

Das, K.; Clark, A.D.; Lewi, P.J.; Heeres, J.; De Jonge, M.R.; Koymans, L.M.; Vinkers, H.M.; Daeyaert, F.; Ludovici, D.W.; Kukla, M.J.; De Corte, B.; Kavash, R.W.; Ho, C.Y.; Ye, H.; Lichtenstein, M.A.; Andries, K.; Pauwels, R.; Boyer, P.L.; Clark, P.; Hughes, S.H.; Janssen, P.A.; Arnold, E.

doi:10.2210/pdb1s6q/pdb

Macromolecule Content

Total Structure Weight: 115112.13
Atom Count: 8052
Residue Count: 990
Unique protein chains: 2

1S6Q

CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) IN COMPLEX WITH JANSSEN-R147681

DOI: 10.2210/pdb1S6Q/pdb

Classification: TRANSFERASE
Organism(s): Human immunodeficiency virus type 1 group M subtype B
Expression System: Escherichia coli
Mutation(s): 2

Deposited: 2004-01-26 Released: 2004-05-11
Deposition Author(s): Das, K., Arnold, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3 Å
R-Value Free: 0.294
R-Value Work: 0.246

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Roles of Conformational and Positional Adaptability in Structure-Based Design of TMC125-R165335 (Etravirine) and Related Non-nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent and Effective against Wild-Type and Drug-Resistant HIV-1 Variants.

Das, K., Clark, A.D., Lewi, P.J., Heeres, J., De Jonge, M.R., Koymans, L.M., Vinkers, H.M., Daeyaert, F., Ludovici, D.W., Kukla, M.J., De Corte, B., Kavash, R.W., Ho, C.Y., Ye, H., Lichtenstein, M.A., Andries, K., Pauwels, R., Boyer, P.L., Clark, P., Hughes, S.H., Janssen, P.A., Arnold, E.

(2004) J.Med.Chem. 47: 2550-2560

PubMed: 15115397 Search on PubMed
DOI: 10.1021/jm030558s
Primary Citation of Related Structures:
1S9G, 1SV5, 1SUQ, 1S9E, 1S6P
Also Cited By: 4G1Q, 5TXP, 5TXO, 5TXN, 5TXM, 5TXL, 3V81, 3V6D, 3V4I, 3QO9, 3BGR, 2ZE2, 2ZD1, 2IC3, 2IAJ

PubMed Abstract:

Anti-AIDS drug candidate and non-nucleoside reverse transcriptase inhibitor (NNRTI) TMC125-R165335 (etravirine) caused an initial drop in viral load similar to that observed with a five-drug combination in naïve patients and retains potency in patients infected with NNRTI-resistant HIV-1 variants. TMC125-R165335 and related anti-AIDS drug candidates can bind the enzyme RT in multiple conformations and thereby escape the effects of drug-resistance mutations. Structural studies showed that this inhibitor and other diarylpyrimidine (DAPY) analogues can adapt to changes in the NNRTI-binding pocket in several ways: (1). DAPY analogues can bind in at least two conformationally distinct modes; (2). within a given binding mode, torsional flexibility ("wiggling") of DAPY analogues permits access to numerous conformational variants; and (3). the compact design of the DAPY analogues permits significant repositioning and reorientation (translation and rotation) within the pocket ("jiggling"). Such adaptations appear to be critical for potency against wild-type and a wide range of drug-resistant mutant HIV-1 RTs. Exploitation of favorable components of inhibitor conformational flexibility (such as torsional flexibility about strategically located chemical bonds) can be a powerful drug design concept, especially for designing drugs that will be effective against rapidly mutating targets.

Related Citations:

Structure of HIV-1 Reverse Transcriptase in a Complex with the Non-Nucleoside Inhibitor Alpha-Apa R 95845 at 2.8 A Resolution
Ding, J.,Das, K.,Tantillo, C.,Zhang, W.,Clark Jr., A.D.,Jessen, S.,Lu, X.,Hsiou, Y.,Jacobo-Molina, A.,Andries, K.,Pauwels, R.,Moereels, H.,Koymans, L.,Janssen, P.A.J.,Smith Jr., R.H.,Kroeger Koepke, M.,Michejda, C.J.,Hughes, S.H.,Arnold, E.
(1995) Structure 3: 365
Crystal Structures of 8-Cl and 9-Cl TIBO Complexed with Wild-Type HIV-1 RT and 8-Cl TIBO Complexed with the Tyr181Cys HIV-1 RT Drug-Resistant Mutant
Das, K.,Ding, J.,Hsiou, Y.,Clark Jr., A.D.,Moereels, H.,Koymans, L.,Andries, K.,Pauwels, R.,Janssen, P.A.,Boyer, P.L.,Clark, P.,Smith Jr., R.H.,Kroeger Smith, M.B.,Michejda, C.J.,Hughes, S.H.,Arnold, E.
(1996) J.Mol.Biol. 264: 1085
Evolution of Anti-HIV Drug Candidates. Part 3: Diarylpyrimidine (Dapy) Analogues
Ludovici, D.W.,De Corte, B.L.,Kukla, M.J.,Ye, H.,Ho, C.Y.,Lichtenstein, M.A.,Kavash, R.W.,Andries, K.,De Bethune, M.,Azijn, H.,Pauwels, R.,Lewi, P.J.,Heeres, J.,Koymans, L.M.,De Jonge, M.R.,Van Aken, K.J.,Daeyaert, F.F.,Das, K.,Arnold, E.,Janssen, P.A.
(2001) Bioorg.Med.Chem.Lett. 11: 2235
Structure and Functional Implications of the Polymerase Active Site Region in a Complex of HIV-1 RT with a Double-Stranded DNA Template-Primer and an Antibody Fab Fragment at 2.8 A Resolution
Ding, J.,Das, K.,Hsiou, Y.,Sarafianos, S.G.,Clark Jr., A.D.,Jacobo-Molina, A.,Tantillo, C.,Hughes, S.H.,Arnold, E.
(1998) J.Mol.Biol. 284: 1095
Structure of HIV-1 RT/TIBO R 86183 Complex Reveals Similarity in the Binding of Diverse Nonnucleoside Inhibitors
Ding, J.,Das, K.,Moereels, H.,Koymans, L.,Andries, K.,Janssen, P.A.J.,Hughes, S.H.,Arnold, E.
(1995) Nat.Struct.Mol.Biol. 2: 407

Organizational Affiliation:

Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
POL polyprotein [Contains: Reverse transcriptase]	A	560	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 1 Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB: P03366
Protein Feature View Full Protein Feature View for P03366

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
POL polyprotein [Contains: Reverse transcriptase]	B	430	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 1 Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB: P03366
Protein Feature View Full Protein Feature View for P03366

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
TPB Query on TPB Download SDF File Download CCD File	A	4-[4-(2,4,6-TRIMETHYL-PHENYLAMINO)-PYRIMIDIN-2-YLAMINO]-BENZONITRILE C₂₀ H₁₉ N₅ ILAYIAGXTHKHNT-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3 Å
R-Value Free: 0.294
R-Value Work: 0.246
Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 228.300	α = 90.00
b = 69.600	β = 106.30
c = 105.300	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
CNS	refinement
X-PLOR	phasing
SCALEPACK	data scaling
X-PLOR	model building

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

Deposited Date: 2004-01-26
Released Date: 2004-05-11
Deposition Author(s): Das, K., Arnold, E.

Revision History

Version 1.0: 2004-05-11
Type: Initial release
Version 1.1: 2008-04-29
Type: Version format compliance
Version 1.2: 2011-07-13
Type: Version format compliance

Prepare Data

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Deposit Data

Deposition Help & Resources

146266 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

1S6Q

CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) IN COMPLEX WITH JANSSEN-R147681

Roles of Conformational and Positional Adaptability in Structure-Based Design of TMC125-R165335 (Etravirine) and Related Non-nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent and Effective against Wild-Type and Drug-Resistant HIV-1 Variants.

Entity ID: 1

Entity ID: 2

Experimental Data

Structure Validation

Deposition Data

Revision History