6AKY | pdb_00006aky

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 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.275 (Depositor), 0.280 (DCC) 
  • R-Value Observed: 
    0.275 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acs.jmedchem.8b01077
  • Primary Citation Related Structures: 
    6AKX, 6AKY

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 44.82 kDa 
  • Atom Count: 2,706 
  • Modeled Residue Count: 340 
  • Deposited Residue Count: 381 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5381Homo sapiensClostridium pasteurianumMutation(s): 4 
Gene Names: CCR5CMKBR5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P00268 (Clostridium pasteurianum)
Explore P00268 
Go to UniProtKB:  P00268
Find proteins for P51681 (Homo sapiens)
Explore P51681 
Go to UniProtKB:  P51681
PHAROS:  P51681
GTEx:  ENSG00000160791 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00268P51681
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A4X

Query on A4X



Download:Ideal Coordinates CCD File
D [auth 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
OLC

Query on OLC



Download:Ideal Coordinates CCD File
C [auth A](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.283 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.275 (Depositor), 0.280 (DCC) 
  • R-Value Observed: 0.275 (Depositor) 
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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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-11-21
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary