6C1Q

Crystal structure of human C5a receptor in complex with an orthosteric antagonist PMX53 and an allosteric antagonist NDT9513727


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Orthosteric and allosteric action of the C5a receptor antagonists.

Liu, H.Kim, H.R.Deepak, R.N.V.K.Wang, L.Chung, K.Y.Fan, H.Wei, Z.Zhang, C.

(2018) Nat. Struct. Mol. Biol. 25: 472-481

  • DOI: 10.1038/s41594-018-0067-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The C5a receptor (C5aR) is a G-protein-coupled receptor (GPCR) that can induce strong inflammatory response to the anaphylatoxin C5a. Targeting C5aR has emerged as a novel anti-inflammatory therapeutic method. However, developing potent C5aR antagoni ...

    The C5a receptor (C5aR) is a G-protein-coupled receptor (GPCR) that can induce strong inflammatory response to the anaphylatoxin C5a. Targeting C5aR has emerged as a novel anti-inflammatory therapeutic method. However, developing potent C5aR antagonists as drugs has proven difficult. Here, we report two crystal structures of human C5aR in ternary complexes with the peptide antagonist PMX53 and a non-peptide antagonist, either avacopan or NDT9513727. The structures, together with other biophysical, computational docking and cell-based signaling data, reveal the orthosteric action of PMX53 and its effect of stabilizing the C5aR structure, as well as the allosteric action of chemically diverse non-peptide C5aR antagonists with different binding poses. Structural comparison analysis suggests the presence of similar allosteric sites in other GPCRs. We also discuss critical structural features of C5aR in activation, including a novel conformation of helix 8. On the basis of our results, we suggest novel strategies for developing C5aR-targeting drugs.


    Organizational Affiliation

    School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea.,Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Biology, Southern University of Science and Technology, Shenzhen, China.,Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA. chengzh@pitt.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Soluble cytochrome b562, C5a anaphylatoxin chemotactic receptor 1 chimera
B
422Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: cybC, C5AR1 (C5AR, C5R1)
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P21730 (Homo sapiens)
Go to Gene View: C5AR1
Go to UniProtKB:  P21730
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PMX53
L
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9P2
Query on 9P2

Download SDF File 
Download CCD File 
B
1-(1,3-benzodioxol-5-yl)-~{N}-(1,3-benzodioxol-5-ylmethyl)-~{N}-[(3-butyl-2,5-diphenyl-imidazol-4-yl)methyl]methanamine
C36 H35 N3 O4
ITACCRHKSPSKKL-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002303
Query on PRD_002303
LPMX53Cyclic peptide / 

--

Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
B
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.369α = 90.00
b = 52.558β = 107.75
c = 84.503γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-06-20
    Type: Data collection, Database references