1KLM

HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH BHAP U-90152


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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.

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

(1997) Proc Natl Acad Sci U S A 94: 3984-3989

  • DOI: 10.1073/pnas.94.8.3984
  • Primary Citation of Related Structures:  
    1KLM

  • PubMed Abstract: 
  • The viral reverse transcriptase (RT) provides an attractive target in the search for anti-HIV therapies. The nonnucleoside inhibitors (NNIs) are a diverse set of compounds (usually HIV-1 specific) that function by distorting the polymerase active site upon binding in a nearby pocket ...

    The viral reverse transcriptase (RT) provides an attractive target in the search for anti-HIV therapies. The nonnucleoside inhibitors (NNIs) are a diverse set of compounds (usually HIV-1 specific) that function by distorting the polymerase active site upon binding in a nearby pocket. Despite being potent and of generally low toxicity, their clinical use has been limited by rapid selection for resistant viral populations. The 2.65-A resolution structure of the complex between HIV-1 RT and the bis(heteroaryl)piperazine (BHAP) NNI, 1-(5-methanesulfonamido-1H-indol-2-yl-carbonyl)-4- [3-(1-methyl-ethylamino) pyridinyl] piperazine (U-90152), reveals the inhibitor conformation and bound water molecules. The bulky U-90152 molecule occupies the same pocket as other NNIs, but the complex is stabilized quite differently, in particular by hydrogen bonding to the main chain of Lys-103 and extensive hydrophobic contacts with Pro-236. These interactions rationalize observed resistance mutations, notably Pro-236-Leu, which occurs characteristically for BHAPs. When bound, part of U-90152 protrudes into the solvent creating a channel between Pro-236 and the polypeptide segments 225-226 and 105-106, giving the first clear evidence of the entry mode for NNIs. The structure allows prediction of binding modes for related inhibitors [(altrylamino)piperidine-BHAPs] and suggests changes to U-90152, such as the addition of a 6 amino group to the pyridine ring, which may make binding more resilient to mutations in the RT. The observation of novel hydrogen bonding to the protein main chain may provide lessons for the improvement of quite different inhibitors.


    Related Citations: 
    • 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
    • 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., Stammers, D.
      (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., Jones, E.Y., Stuart, D.I.
      (1994) J Mol Biol 242: 586

    Organizational Affiliation

    Laboratory of Molecular Biophysics, Oxford, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASEA560Human immunodeficiency virus 1Mutation(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)
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASEB440Human immunodeficiency virus 1Mutation(s): 0 
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)
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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPP (Subject of Investigation/LOI)
Query on SPP

Download Ideal Coordinates CCD File 
C [auth A](1-(5-METHANSULPHONAMIDO-1H-INDOL-2-YL-CARBONYL)4-[METHYLAMINO)PYRIDINYL]PIPERAZINE
C22 H28 N6 O3 S
WHBIGIKBNXZKFE-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
AL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
SPP BindingDB:  1KLM IC50: min: 1.3, max: 8320 (nM) from 16 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.8α = 90
b = 109.4β = 90
c = 72γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-03-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-07-18
    Changes: Non-polymer description