6AKY

The Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 34


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.275 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Based Design of 1-Heteroaryl-1,3-propanediamine Derivatives as a Novel Series of CC-Chemokine Receptor 5 Antagonists.

Peng, P.Chen, H.Zhu, Y.Wang, Z.Li, J.Luo, R.H.Wang, J.Chen, L.Yang, L.M.Jiang, H.Xie, X.Wu, B.Zheng, Y.T.Liu, H.

(2018) J. Med. Chem. 61: 9621-9636

  • DOI: 10.1021/acs.jmedchem.8b01077
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CC-chemokine receptor 5 (CCR5) is an attractive target for preventing the entry of human immunodeficiency virus 1 (HIV-1) into human host cells. Maraviroc is the only CCR5 antagonist, and it was marketed in 2007. To overcome the shortcomings of marav ...

    CC-chemokine receptor 5 (CCR5) is an attractive target for preventing the entry of human immunodeficiency virus 1 (HIV-1) into human host cells. Maraviroc is the only CCR5 antagonist, and it was marketed in 2007. To overcome the shortcomings of maraviroc, structure-based drug design was performed to minimize CYP450 inhibition and to enhance anti-HIV potency and bioavailability. Thirty-four novel 1-heteroaryl-1,3-propanediamine derivatives (1-34) were synthesized, displaying CCR5-antagonist activities in the 2.3-296.4 nM range. Among these, compounds 21 and 34 were the most potent CCR5 antagonists, with excellent in vitro anti-HIV-1 activity, low cytotoxicity, and an acceptable pharmacokinetic profile. Furthermore, the X-ray crystal structures of compounds 21 and 34 bound to CCR5 were determined at 2.8 Å resolution. Compound 34 exhibited no CYP450-inhibition activity at 25 μM, which overcomes the potential drug-drug interaction of maraviroc. Compound 34 represents a promising drug candidate for HIV-infection treatment.


    Organizational Affiliation

    Key Laboratory of Bioactive Peptides of Yunnan Province, Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases , Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , Yunnan 650223 , China.,University of Chinese Academy of Sciences , Number 19A Yuquan Road , Beijing 100049 , China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5
A
381Homo sapiensClostridium pasteurianum
This entity is chimeric
Mutation(s): 4 
Gene Names: CCR5 (CMKBR5),
Find proteins for P51681 (Homo sapiens)
Go to Gene View: CCR5
Go to UniProtKB:  P51681
Find proteins for P00268 (Clostridium pasteurianum)
Go to UniProtKB:  P00268
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
A4X
Query on A4X

Download SDF File 
Download CCD File 
A
4,4-difluoro-N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]octan-8-yl}-1-(thiophen-3-yl)propyl]cyclohexane-1-carboxamide
C27 H39 F2 N5 O S
KESMRFWRGXZDEF-KIHHCIJBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.275 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.585α = 90.00
b = 101.483β = 90.00
c = 136.569γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-09-04 
  • Released Date: 2018-10-24 
  • Deposition Author(s): Zhu, Y., Zhao, Q., Wu, B.

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-11-21
    Type: Data collection, Database references