1HNV

STRUCTURE OF HIV-1 RT(SLASH)TIBO R 86183 COMPLEX REVEALS SIMILARITY IN THE BINDING OF DIVERSE NONNUCLEOSIDE INHIBITORS

PDB DOI: 10.2210/pdb1HNV/pdb

Classification: NUCLEOTIDYLTRANSFERASE
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1995-03-30 Released: 1995-07-10
Deposition Author(s): Das, K., Ding, J., Arnold, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.356
R-Value Work: 0.249
R-Value Observed: 0.249

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

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., Hughes, S.H., Arnold, E.

(1995) Nat Struct Biol 2: 407-415

PubMed: 7545077 Search on PubMed
DOI: 10.1038/nsb0595-407
Primary Citation of Related Structures:
1HNV

PubMed Abstract:

We report the structure of HIV-1 reverse transcriptase (RT) complexed with the nonnucleoside inhibitor TIBO R 86183 at 3.0 A resolution. Comparing this structure with those of complexes of HIV-1 RT/alpha-APA R 95845 and HIV-1 RT/nevirapine provides a basis for understanding the nature of nonnucleoside inhibitor binding, the structure of the binding site and the interactions between the bound inhibitors and surrounding amino acid residues as well as for understanding mechanisms of inhibition by and resistance to nonnucleoside inhibitors. All three inhibitors considered assume a similar butterfly-like shape and bind to HIV-1 RT in a very similar way. Important differences occur in the conformation of amino acid residues that form the binding pocket.

Related Citations:

Structure of HIV-1 Reverse Transcriptase in a Complex with the Nonnucleoside Inhibitor Alpha-Apa R95845 at 2.8 Angstroms Resolution
Ding, J., Das, K., Tantillo, C., Zhang, W., Clark Junior, A.D., Jessen, S., Lu, X., Hsiou, Y., Jacobo-Molina, A., Andries, K., Pauwels, R., Moereels, H., Koymans, L., Janssen, P.A.J., Smith Junior, R.H., Koepke, M.K., Michejda, C.J., Hughes, S.H., Arnold, E.
(1995) Structure 3: 365

Buried Surface Analysis of HIV-1 Reverse Transcriptase P66(Slash)P51 Heterodimer and its Interaction with DsDNA Template(Slash)Primer
Ding, J., Jacobo-Molina, A., Tantillo, C., Lu, X., Nanni, R.G., Arnold, E.
(1994) J Mol Recognit 7: 157

Locations of Anti-Aids Drug Binding Sites and Resistance Mutations in the Three-Dimensional Structure of HIV-1 Reverse Transcriptase: Implications for Mechanisms of Drug Inhibition and Resistance
Tantillo, C., Ding, J., Jacobo-Molina, A., Nanni, R.G., Boyer, P.L., Hughes, S.H., Pauwels, R., Andries, K., Janssen, P.A.J., Arnold, E.
(1994) J Mol Biol 243: 369

Crystal Structure of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed with Double-Stranded DNA at 3.0 Angstroms Resolution Shows Bent DNA
Jacobo-Molina, A., Ding, J., Nanni, R.G., Clark Junior, A.D., Lu, X., Tantillo, C., Williams, R.L., Kamer, G., Ferris, A.L., Clark, P., Hizi, A., Hughes, S.H., Arnold, E.
(1993) Proc Natl Acad Sci U S A 90: 6320

Review of HIV-1 Reverse Transcriptase Three-Dimensional Structure: Implications for Drug Design
Nanni, R.G., Ding, J., Jacobo-Molina, A., Hughes, S.H., Arnold, E.
(1993) Perspect Drug Discov Des 1: 129

Structure of HIV-1 Reverse Transcriptase(Slash)DNA Complex at 7 Angstroms Resolution Showing Active Site Locations
Arnold, E., Jacobo-Molina, A., Nanni, R.G., Williams, R.L., Lu, X., Ding, J., Clark Junior, A.D., Zhang, A., Ferris, A.L., Clark, P., Hizi, A., Hughes, S.H.
(1992) Nature 357: 85

Crystals of a Ternary Complex of Human Immunodeficiency Virus Type 1 Reverse Transcriptase with a Monoclonal Antibody Fab Fragment and Double-Stranded DNA Diffract X-Rays to 3.5 Angstroms Resolution
Jacobo-Molina, A., Clark Junior, A.D., Williams, R.L., Nanni, R.G., Clark, P., Ferris, A.L., Hughes, S.H., Arnold, E.
(1991) Proc Natl Acad Sci U S A 88: 10895

Organizational Affiliation:

Center for Advanced Biotechnology and Medicine (CABM), Piscataway, New Jersey 08854-5638, USA.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P66)	A	558	Human immunodeficiency virus 1	Mutation(s): 0 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)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03366
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 REVERSE TRANSCRIPTASE (SUBUNIT P51)	B	427	Human immunodeficiency virus 1	Mutation(s): 0 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)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03366
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TBO Query on TBO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	5-CHLORO-8-METHYL-7-(3-METHYL-BUT-2-ENYL)-6,7,8,9-TETRAHYDRO-2H-2,7,9A-TRIAZA-BENZO[CD]AZULENE-1-THIONE C₁₆ H₂₀ Cl N₃ S ZNFFMCYSMBXZQU-NSHDSACASA-N		Ligand Interaction