6AKY

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.275 
  • R-Value Observed: 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:  
    6AKY, 6AKX

  • 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: 

    University of Chinese Academy of Sciences , Number 19A Yuquan Road , Beijing 100049 , China.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5A381Homo sapiens, Clostridium pasteurianumMutation(s): 4 
Gene Names: CCR5, CMKBR5
Find proteins for P51681 (Homo sapiens)
Explore P51681 
Go to UniProtKB:  P51681
NIH Common Fund Data Resources
PHAROS  P51681
GTEx  ENSG00000160791
Find proteins for P00268 (Clostridium pasteurianum)
Explore P00268 
Go to UniProtKB:  P00268
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A4X
Query on A4X
Download Ideal Coordinates 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
OLC
Query on OLC
Download Ideal Coordinates CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.275 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.585α = 90
b = 101.483β = 90
c = 136.569γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

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
    Changes: Data collection, Database references