6BZ2

Crystal structure of wild-type HIV-1 protease with a novel HIV-1 inhibitor GRL-14213A of 6-5-5-ring fused crown-like tetrahydropyranofuran as the P2-ligand, a cyclopropylaminobenzothiazole as the P2'-ligand and 3,5-difluorophenylmethyl as the P1-ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Design of Highly Potent, Dual-Acting and Central-Nervous-System-Penetrating HIV-1 Protease Inhibitors with Excellent Potency against Multidrug-Resistant HIV-1 Variants.

Ghosh, A.K.Rao, K.V.Nyalapatla, P.R.Kovela, S.Brindisi, M.Osswald, H.L.Sekhara Reddy, B.Agniswamy, J.Wang, Y.F.Aoki, M.Hattori, S.I.Weber, I.T.Mitsuya, H.

(2018) ChemMedChem 13: 803-815

  • DOI: 10.1002/cmdc.201700824

  • PubMed Abstract: 
  • We report here the design, synthesis, X-ray-structural, and biological studies of an exceptionally potent HIV-1 protease inhibitor 5. In this inhibitor, we incorporated an unprecedented structure-based designed 6-5-5-ring fused crown-like tetrahydrop ...

    We report here the design, synthesis, X-ray-structural, and biological studies of an exceptionally potent HIV-1 protease inhibitor 5. In this inhibitor, we incorporated an unprecedented structure-based designed 6-5-5-ring fused crown-like tetrahydropyranofuran as the P2-ligand, a cyclopropylaminobenzothiazole as the P2'-ligand and 3,5-difluorophenylmethyl as the P1-ligand. The resulting inhibitor 5, exhibited exceptional HIV-1 inhibitory and antiviral potency at picomolar level. Furthermore, it displayed antiviral IC50 values in picomolar range against a wide panel of highly multidrug-resistant HIV-1 variants. The inhibitor shows an extremely high genetic barrier against the emergence of drug-resistant variants. It also showed extremely potent dimerization inhibitory activity and penetrated CNS favourably. We have determined a high resolution X-ray structure of inhibitor 5-bound HIV-1 complex which provided molecular insight into the unprecedented activity profiles.


    Organizational Affiliation

    Purdue University, Departments of Chemistry and Medicinal Chemistry, 560 Oval Drive, 47907, West Lafayette, UNITED STATES.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus type 1 group M subtype BMutation(s): 5 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Small Molecules
Ligands 4 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
ACT
Query on ACT

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Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
7OA
Query on 7OA

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Download CCD File 
B
(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]carbamate
C33 H40 F2 N4 O7 S2
ARWGTMGGJGADTI-VFGYXJDYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.043α = 90.00
b = 86.426β = 90.00
c = 45.932γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
SHELXL-97refinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM53386
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM62920
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japana Grant-in-Aid for Scientific Research (Priority Areas)
the Ministry of Health, Welfare, and Labor of JapanJapana Grant for Promotion of AIDS Research
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanthe Grant to the Cooperative Research Project on Clinical and Epidemiological Studies of Emerging and Reemerging Infectious Diseases (Renkei Jigyo)

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-28
    Type: Data collection, Database references
  • Version 1.2: 2018-05-02
    Type: Data collection, Database references