PDBsum entry 1rt5

Nucleotidyltransferase

PDB id: 1rt5

Contents

Protein chains

537 a.a. *

406 a.a. *

Ligands

PO4

UC2

Waters ×5

* Residue conservation analysis

References listed in PDB file

Key reference

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

Abstract

The carboxanilides are nonnucleoside inhibitors (NNIs) of HIV-1 reverse transcriptase (RT), of potential clinical importance. The compounds differ in potency and in their retention of potency in the face of drug resistance mutations. Whereas UC-84, the prototype compound, only weakly inhibits many RTs bearing single point resistance mutations, inhibition by UC-781 is little affected. It has been proposed that UC-38 and UC-781 may form quaternary complexes with RT at a site other than the known binding pocket of other NNIs. X-ray crystal structures of four HIV-1 RT-carboxanilide complexes (UC-10, UC-38, UC-84, and UC-781) reported here reveal that all four inhibitors bind in the usual NNI site, forming binary 1:1 complexes with RT in the absence of substrates with the amide/thioamide bond in cis conformations. For all four complexes the anilide rings of the inhibitors overlap aromatic rings of many other NNIs bound to RT. In contrast, the second rings of UC-10, UC-84, and UC-781 do not bind in equivalent positions to those of other "two-ring" NNIs such as alpha-APA or HEPT derivatives. The binding modes most closely resemble that of the structurally dissimilar NNI, Cl-TIBO, with a common hydrogen bond between each carboxanilide NH- group and the main-chain carbonyl oxygen of Lys101. The binding modes differ slightly between the UC-10/UC-781 and UC-38/UC-84 pairs of compounds, apparently related to the shorter isopropylmethanoyl substituents of the anilide rings of UC-38/UC-84, which draws these rings closer to residues Tyr181 and Tyr188. This in turn explains the differences in the effect of mutated residues on the binding of these compounds.

Secondary reference #1

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 #2

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 #3

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 #4

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 #5

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 #6

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 #7

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 #8

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