PDBsum entry 1ep4

Transferase

PDB id: 1ep4

Contents

Protein chains

523 a.a. *

395 a.a. *

Ligands

S11

Waters ×197

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Binding of the second generation non-Nucleoside inhibitor s-1153 to HIV-1 reverse transcriptase involves extensive main chain hydrogen bonding.

Authors

J.Ren, C.Nichols, L.E.Bird, T.Fujiwara, H.Sugimoto, D.I.Stuart, D.K.Stammers.

Ref.

J Biol Chem, 2000, 275, 14316-14320. [DOI no: 10.1074/jbc.275.19.14316]

PubMed id

10799511

Abstract

S-1153 (AG1549) is perhaps the most promising non-nucleoside inhibitor of HIV-1 reverse transcriptase currently under development as a potential anti-AIDS drug, because it has a favorable profile of resilience to many drug resistance mutations. We have determined the crystal structure of S-1153 in a complex with HIV-1 reverse transcriptase. The complex possesses some novel features, including an extensive network of hydrogen bonds involving the main chain of residues 101, 103, and 236 of the p66 reverse transcriptase subunit. Such interactions are unlikely to be disrupted by side chain mutations. The reverse transcriptase/S-1153 complex suggests different ways in which resilience to mutations in the non-nucleoside inhibitors of reverse transcriptase binding site can be achieved.

Figure 1.
Fig. 1. Simulated annealing omit electron density map showing the bound S-1153 in the NNRTI pocket of HIV-1 RT. The map is contoured at 3 .

Figure 3.
Fig. 3. Schematic diagram showing the intermolecular interactions between S-1153 and the surrounding residues of HIV-1 RT. The pink spheres represent water molecules in contact with the inhibitor. Residues that contact the NNRTI with a minimum interatomic distance of 3.6Å are shown in green, whereas other residues lining the binding pocket are shown in blue. The individual distances between the NNRTI and the protein atoms are shown as dashed lines (distances less than or equal to 3.3 Å are in pink; distances between 3.3 and 3.6 Å are in light blue; hydrogen bonds are shown together with distances in black).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 14316-14320) copyright 2000.

Secondary reference #1

Title

Phenylethylthiazolylthiourea (pett) non-Nucleoside inhibitors of HIV-1 and HIV-2 reverse transcriptases. Structural and biochemical analyses.

Authors

J.Ren, J.Diprose, J.Warren, R.M.Esnouf, L.E.Bird, S.Ikemizu, M.Slater, J.Milton, J.Balzarini, D.I.Stuart, D.K.Stammers.

Ref.

J Biol Chem, 2000, 275, 5633-5639. [DOI no: 10.1074/jbc.275.8.5633]

PubMed id

10681546

Figure 1.
Fig. 1. Simulated annealing omit electron density maps showing the bound inhibitors at the NNRTI pocket of HIV-1 RT. a, PETT-1; b, PETT-2. The maps are contoured at 4 .

Figure 4.
Fig. 4. . Schematic diagrams showing the intermolecular interactions between PETT inhibitors (in red) and the surrounding residues of HIV-1 RT for (a) PETT-1 and (b) PETT-2. Residues that contact the NNRTI with a minimum inter-atomic distance of 3.6 Å are shown in green, whereas other residues lining the binding pocket are shown in blue. The individual distances between the NNRTI and the protein atoms are shown as dashed lines (distances 3.3 Å in pink, 3.3 Å < distances 3.6 Å in light blue). Hydrogen bonds together with their distances are shown in black.

The above figures are reproduced from the cited reference with permission from the ASBMB

Secondary reference #2

Title

Crystallographic analysis of the binding modes of thiazoloisoindolinone non-Nucleoside inhibitors to HIV-1 reverse transcriptase and comparison with modeling studies.

Authors

J.Ren, R.M.Esnouf, A.L.Hopkins, D.I.Stuart, D.K.Stammers.

Ref.

J Med Chem, 1999, 42, 3845-3851. [DOI no: 10.1021/jm990275t]

PubMed id

10508433

Secondary reference #3

Title

Design of mkc-442 (emivirine) analogues with improved activity against drug-Resistant HIV mutants.

Authors

A.L.Hopkins, J.Ren, H.Tanaka, M.Baba, M.Okamato, D.I.Stuart, D.K.Stammers.

Ref.

J Med Chem, 1999, 42, 4500-4505. [DOI no: 10.1021/jm990192c]

PubMed id

10579814

Secondary reference #4

Title

Crystal structures of HIV-1 reverse transcriptase in complex with carboxanilide derivatives.

Authors

J.Ren, R.M.Esnouf, A.L.Hopkins, J.Warren, J.Balzarini, D.I.Stuart, D.K.Stammers.

Ref.

Biochemistry, 1998, 37, 14394-14403. [DOI no: 10.1021/bi981309m]

PubMed id

9772165

Secondary reference #5

Title

3'-Azido-3'-Deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes.

Authors

J.Ren, R.M.Esnouf, A.L.Hopkins, E.Y.Jones, I.Kirby, J.Keeling, C.K.Ross, B.A.Larder, D.I.Stuart, D.K.Stammers.

Ref.

Proc Natl Acad Sci U S A, 1998, 95, 9518-9523. [DOI no: 10.1073/pnas.95.16.9518]

PubMed id

9689112

Figure 1.
Fig. 1. Overall structure and drug resistance mutation sites of the RT heterodimer. (Top) The p66 subunit is drawn in dark gray and p51 in light gray. NI resistance mutation sites (26) are shown as green spheres, with RTMC and L74V sites highlighted in yellow. In the p51 subunit, residues 215 and 219 are disordered; their positions are not shown. NNI resistance mutation sites (27) are shown as blue spheres. The three polymerase active site aspartate residues and the bound NNI are shown in red and magenta, respectively. Double-stranded DNA (shown as a spiral ladder with the template strand in green and the primer in red) was modeled into our RT-nevirapine structure (6) from the C and phosphate coordinates of the RT-DNA-Fab complex (5) by superimposing the p66 palm domain of the two structures. (Bottom) A close-up view of the polymerase active site and the drug resistance mutation sites in the p66 subunit. The coloring scheme is the same as in the top panel; however, the side chains for mutated residues are shown in ball-and-stick representation and the van der Waals surface for the bound NNI (nevirapine) is shown semitransparent.

Figure 3.
Fig. 3. The NNI binding site and polymerase active site. (a) A stereodiagram showing the superposition of the NNI binding site in RTMC and wild-type RT. The protein backbone is shown by thin sticks. The NNIs (thick bonds) and side chains that have contacts with the NNIs are shown as ball-and-stick representations. The RTMC is colored in green with residue 181 and the bound 1051U91 highlighted in red. The wild-type RT is colored in blue with residue 181 and bound 1051U91 highlighted in yellow. (b) A stereodiagram of the superposition of the active sites in RTMC (green), the wild type unliganded (red), and six NNI-bound RT structures (blue for RT-1051U91, gray for others) showing the structural changes at the active site in RTMC caused by 215 and 219 mutations. The C trace and side chains for residues 110, 185, 186, 215, and 219 are shown for RTMC, wild-type unliganded RT, and RT-1051U91; the C traces only are shown for RT-Cl-TIBO, RT-BHAP, RT-nevirapine, RT-MKC-442, and RT- -APA. In the p51 subunit, residues 215 and 219 are disordered whereas residues 67 and 70 do not show significant rearrangement from the wild-type p51.

Secondary reference #6

Title

Continuous and discontinuous changes in the unit cell of HIV-1 reverse transcriptase crystals on dehydration.

Authors

R.M.Esnouf, J.Ren, E.F.Garman, D.O.Somers, C.K.Ross, E.Y.Jones, D.K.Stammers, D.I.Stuart.

Ref.

Acta Crystallogr D Biol Crystallogr, 1998, 54, 938-953. [DOI no: 10.1107/S0907444998004284]

PubMed id

9757109

Figure 2.
Fig. 2. Diffraction images from the crystal mounted in an imperfectly sealed capillary tube. Images are numbered and labelled with the cell foms contributing to the diffraction. The time between consecutive images is approximately 20 min. Figure prodced using PSIMAGE (R. M. Esnouf, unpublished program).

Figure 7.
Fig. 7. 'Front' and 'back' views showing areas of crystal contacts on the surface of the RT eterodimer for each cll form. Grey areas of th suface make no crstal contacts. The coloured contact patches can be related to specific crystallographic symmetry operations using Table 3, the pale shade of eac hue contacting the corresponding dark shade in a ymmetry-related molecule, and vice versa.

The above figures are reproduced from the cited reference with permission from the IUCr

Secondary reference #7

Title

Unique features in the structure of the complex between HIV-1 reverse transcriptase and the bis(heteroaryl)piperazine (bhap) u-90152 explain resistance mutations for this nonnucleoside inhibitor.

Authors

R.M.Esnouf, J.Ren, A.L.Hopkins, C.K.Ross, E.Y.Jones, D.K.Stammers, D.I.Stuart.

Ref.

Proc Natl Acad Sci U S A, 1997, 94, 3984-3989. [DOI no: 10.1073/pnas.94.8.3984]

PubMed id

9108091

Figure 2.
Fig. 2. Stereo diagram showing F[obs] F[calc] omit electron density for U-90152 contoured at 3 U-90152 is shown in ball-and-stick representation and the surrounding protein structure is shown by thin sticks. Residue Tyr-318, which would otherwise obscure the BHAP carbonyl group, is omitted from the figure for clarity.

Figure 4.
Fig. 4. Interactions between the indole ring of U-90152 and Pro-236. U-90152 is shown with thick bonds, residues 235-237 with thin bonds and interatomic distances <3.6 Å by broken lines. With so many interactions it is not surprising that mutations of this residue (such as Pro-236-Leu) disrupt the binding of BHAPs.

Secondary reference #8

Title

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

Authors

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

Ref.

J Med Chem, 1996, 39, 1589-1600. [DOI no: 10.1021/jm960056x]

PubMed id

8648598

Secondary reference #9

Title

The structure of HIV-1 reverse transcriptase complexed with 9-Chloro-Tibo: lessons for inhibitor design.

Authors

J.Ren, R.Esnouf, A.Hopkins, C.Ross, Y.Jones, D.Stammers, D.Stuart.

Ref.

Structure, 1995, 3, 915-926. [DOI no: 10.1016/S0969-2126(01)00226-X]

PubMed id

8535785

Figure 1.
Figure 1. The structure of 9-chloro-TIBO (R82913) showing the numbering of atoms in the ring system and the required stereospecificity of the 5-methyl substituent. Figure 1. The structure of 9-chloro-TIBO (R82913) showing the numbering of atoms in the ring system and the required stereospecificity of the 5-methyl substituent.

Figure 5.
Figure 5. Ribbon diagram of the form E RT/Cl-TIBO complex using colour coding to illustrate the structural variation from the unliganded form E RT structure. Cl-TIBO is shown as a space-filling model. The form E RT/Cl-TIBO model was produced by a nine-domain rigid-body refinement of the form F model on to the partial data set of form E. Hence, some artifactual variation can be detected near the domain boundaries (light blue). Figure 5. Ribbon diagram of the form E RT/Cl-TIBO complex using colour coding to illustrate the structural variation from the unliganded form E RT structure. Cl-TIBO is shown as a space-filling model. The form E RT/Cl-TIBO model was produced by a nine-domain rigid-body refinement of the form F model on to the partial data set of form E. Hence, some artifactual variation can be detected near the domain boundaries (light blue).

The above figures are reproduced from the cited reference with permission from Cell Press

Secondary reference #10

Title

High resolution structures of HIV-1 rt from four rt-Inhibitor complexes.

Authors

J.Ren, R.Esnouf, E.Garman, D.Somers, C.Ross, I.Kirby, J.Keeling, G.Darby, Y.Jones, D.Stuart.

Ref.

Nat Struct Biol, 1995, 2, 293-302.

PubMed id

7540934

Secondary reference #11

Title

Mechanism of inhibition of HIV-1 reverse transcriptase by non-Nucleoside inhibitors.

Authors

R.Esnouf, J.Ren, C.Ross, Y.Jones, D.Stammers, D.Stuart.

Ref.

Nat Struct Biol, 1995, 2, 303-308.

PubMed id

7540935

Secondary reference #12

Title

Crystals of HIV-1 reverse transcriptase diffracting to 2.2 a resolution.

Authors

D.K.Stammers, D.O.Somers, C.K.Ross, I.Kirby, P.H.Ray, J.E.Wilson, M.Norman, J.S.Ren, R.M.Esnouf, E.F.Garman.

Ref.

J Mol Biol, 1994, 242, 586-588.

PubMed id

7523679