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 1
Expression System: Escherichia coli
Mutation(s): Yes

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.294
R-Value Work: 0.246
R-Value Observed: 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
Structures With Same Primary Citation

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 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 Biol 2: 407

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

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

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

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 1	Mutation(s): 1 Gene Names: POL EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Protein Feature View
( Mouse scroll to zoom / Hold left click to move ) Reference Sequence

Find similar proteins by: Sequence | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
POL polyprotein [Contains: Reverse transcriptase]	B	430	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: POL EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Protein Feature View
( Mouse scroll to zoom / Hold left click to move ) Reference Sequence

Small Molecules

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