6DJ2

HIV-1 protease with single mutation L76V in complex with Lopinavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap-Core Interface of HIV-1 Protease.

Wong-Sam, A.Wang, Y.F.Zhang, Y.Ghosh, A.K.Harrison, R.W.Weber, I.T.

(2018) ACS Omega 3: 12132-12140

  • DOI: 10.1021/acsomega.8b01683
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Four HIV-1 protease (PR) inhibitors, clinical inhibitors lopinavir and tipranavir, and two investigational compounds <b>4 </b> and <b>5 </b>, were studied for their effect on the structure and activity of PR with drug-resistant mutation L76V (PR <s ...

    Four HIV-1 protease (PR) inhibitors, clinical inhibitors lopinavir and tipranavir, and two investigational compounds 4 and 5 , were studied for their effect on the structure and activity of PR with drug-resistant mutation L76V (PR L76V ). Compound 5 exhibited the best K i value of 1.9 nM for PR L76V , whereas the other three inhibitors had K i values of 4.5-7.6 nM, 2-3 orders of magnitude worse than for wild-type enzymes. Crystal structures showed only minor differences in interactions of inhibitors with PR L76V compared to wild-type complexes. The shorter side chain of Val76 in the mutant lost hydrophobic interactions with Lys45 and Ile47 in the flap, and with Asp30 and Thr74 in the protein core, consistent with decreased stability. Inhibitors forming additional polar interactions with the flaps or dimer interface of PR L76V were unable to compensate for the decrease in internal hydrophobic contacts. These structures provide insights for inhibitor design.


    Organizational Affiliation

    Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea. Electronic address: chahong@korea.ac.kr.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 106, Taiwan. andyhsu@ntu.edu.tw.,Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand.,Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.,Dipartimento di Scienze della Terra , Università di Pisa , via Santa Maria 53 , 56126 Pisa , Italy.,Division of Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudangiro Ochang, Cheongwongu, Cheongju, Chungbuk 28119, South Korea.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Genmab, Yalelaan 60, 3584 CM Utrecht, Netherlands.,Genmab, Yalelaan 60, 3584 CM Utrecht, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Department of Chemistry and Biochemistry, University of Lethbridge, Alberta T1K 3M4, Canada.,Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica., Taipei, 115, Taiwan.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK. s.s.virdee@dundee.ac.uk.,Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan. bmchinp@ibms.sinica.edu.tw.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand.,Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States.,Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.,Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany.,Institute of Fundamental Sciences and the Riddet Institute, Massey University, Palmerston North 4442, New Zealand.,Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China.,NHC Key Laboratory of Cancer Proteomics & Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China. yonghenc@163.com.,Institute of Neuropathology, University of Zurich, Switzerland.,Institute of Molecular Systems Biology and Department of Health Sciences and Technology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA mr@purdue.edu.,Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.,Institute for Genetics, University of Cologne, Cologne, Germany.,Dipartimento di Farmacia , Università di Pisa , Via Bonanno 6 , 56126 Pisa , Italy.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,CEA, Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Université Paris-Saclay , Gif-sur-Yvette 91190 , France.,SAXS/WAXS, Australian Synchrotron/ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia.,Section of Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, Netherlands.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China. shaofeng@nibs.ac.cn.,Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,Department of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.,Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand emily.parker@vuw.ac.nz g.b.jameson@massey.ac.nz.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.,Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.,Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria.,Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan.,NeCEN, Gorlaeus Laboratories, Leiden University, 2333 CC Leiden, Netherlands.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China. shaofeng@nibs.ac.cn.,Institute for Advanced Biosciences, Keio University, 14-1 Baba-cho, Tsuruoka, Yamagata 997-0035, Japan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan.,National Institute of Biological Sciences, Beijing, China.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 106, Taiwan.,Centro de Química Estrutural, Instituto Superior Técnico , Universidade de Lisboa , Av. Rovisco Pais 1 , 1049-001 Lisboa , Portugal.,Synchrotron SOLEIL , L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette , France.,Laboratory of Biomolecular Research, Division of Biology and Chemistry , Paul Scherrer Institute , 5232 Villigen , Switzerland.,Instituto de Bionanotecnología del NOA, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Santiago del Estero, G4206XCP Santiago del Estero, Argentina.,Section of Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, Einthovenweg 20, 2300 RC Leiden, Netherlands. t.sharp@lumc.nl p.w.h.i.parren@lumc.nl p.gros@uu.nl.,Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand.,Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.,Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. shaofeng@nibs.ac.cn.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300, Taiwan.,Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.,Department of Agricultural Chemistry, National Taiwan University, Taipei, 106, Taiwan. andyhsu@ntu.edu.tw.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. nisimasu@bs.s.u-tokyo.ac.jp nureki@bs.s.u-tokyo.ac.jp.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,McGovern Institute for Brain Research, Cambridge, MA 02139, USA.,Beijing Mingde Zhengkang Technologies Co., Ltd., Beijing, China.,Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan.,Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea; Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.,College of Animal Science and Technology, China Agricultural University, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 protease
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 6 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
AB1
Query on AB1

Download SDF File 
Download CCD File 
B
N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE
ABT-378, LOPINAVIR
C37 H48 N4 O5
KJHKTHWMRKYKJE-SUGCFTRWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 60.011α = 90.00
b = 85.377β = 90.00
c = 46.430γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesGM062920

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release