1RT1

CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH MKC-442

DOI: 10.2210/pdb1RT1/pdb

Classification: NUCLEOTIDYLTRANSFERASE
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 1996-03-16 Released: 1997-04-21
Deposition Author(s): Ren, J., Esnouf, R., Hopkins, A., Willcox, B., Jones, Y., Ross, C., Stammers, D., Stuart, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Work: 0.197
R-Value Observed: 0.197

wwPDB Validation 3D Report Full Report

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

Literature

Complexes of HIV-1 reverse transcriptase with inhibitors of the HEPT series reveal conformational changes relevant to the design of potent non-nucleoside inhibitors.

Hopkins, A.L., Ren, J., Esnouf, R.M., Willcox, B.E., Jones, E.Y., Ross, C., Miyasaka, T., Walker, R.T., Tanaka, H., Stammers, D.K., Stuart, D.I.

(1996) J Med Chem 39: 1589-1600

PubMed: 8648598 Search on PubMed
DOI: 10.1021/jm960056x
Primary Citation of Related Structures:
1RT2, 1RT1

PubMed Abstract:

Crystal structures of HIV-1 reverse transcriptase (RT) complexed with a range of chemically diverse non-nucleoside inhibitors (NNIs) have shown a single pocket in which the inhibitors bind and details of the inhibitor-protein interactions. To delineate the structural requirements for an effective inhibitor, we have determined the structures of three closely related NNIs which vary widely in their potencies. Crystal structures of HIV-1 RT complexed with two very potent inhibitors, MKC-442 and TNK-651, at 2.55 angstroms resolution complement our previous analysis of the complex with the less effective inhibitor, HEPT. These structures reveal conformational changes which correlate with changes in potency. We suggest that a major determinant of increased potency in the analogues of HEPT is an improved interaction between residue Tyr181 in the protein and the 6-benzyl ring of the inhibitors which stabilizes the structure of the complex. This arises through a conformational switching of the protein structure triggered by the steric bulk of the 5-substituent of the inhibitor pyrimidine ring.

Related Citations:

Mechanism of Inhibition of HIV-1 Reverse Transcriptase by Non-Nucleoside Inhibitors
Esnouf, R., Ren, J., Ross, C., Jones, Y., Stammers, D., Stuart, D.
(1995) Nat Struct Biol 2: 303

High Resolution Structures of HIV-1 RT from Four RT-Inhibitor Complexes
Ren, J., Esnouf, R., Garman, E., Somers, D., Ross, C., Kirby, I., Keeling, J., Darby, G., Jones, Y., Stuart, D., al., et
(1995) Nat Struct Biol 2: 293

The Structure of HIV-1 Reverse Transcriptase Complexed with 9-Chloro-TIBO: Lessons for Inhibitor Design
Ren, J., Esnouf, R., Hopkins, A., Ross, C., Jones, Y., Stammers, D., Stuart, D.
(1995) Structure 3: 915

Crystals of HIV-1 Reverse Transcriptase Diffracting to 2.2 A Resolution
Stammers, D.K., Somers, D.O., Ross, C.K., Kirby, I., Ray, P.H., Wilson, J.E., Norman, M., Ren, J.S., Esnouf, R.M., Garman, E.F., al., et
(1994) J Mol Biol 242: 586

Organizational Affiliation:

Laboratory of Molecular Biophysics, Rex Richards Building, Oxford, UK.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 REVERSE TRANSCRIPTASE	A	560	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: HIV-1 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 P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585 Go to UniProtKB: P04585
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 REVERSE TRANSCRIPTASE	B	440	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: HIV-1 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 P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585 Go to UniProtKB: P04585
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MKC Query on MKC Download Ideal Coordinates CCD File SDF format, chain C [A] MOL2 format, chain C [A]	A	6-BENZYL-1-ETHOXYMETHYL-5-ISOPROPYL URACIL C₁₇ H₂₂ N₂ O₃ MLILORUFDVLTSP-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
MKC	EC50: 20 nM BindingDB
MKC	EC50: 4.199999809265137 nM BindingDB
MKC	IC50: 800 nM BindingDB
MKC	IC50 : 8 nM PDBBind
MKC	EC50: 2 nM BindingDB
MKC	EC50: 4 nM BindingDB
MKC	IC50: 8 nM BindingDB
MKC	IC50: 40 nM BindingDB