6GPX

CRYSTAL STRUCTURE OF CCR2A IN COMPLEX WITH MK-0812


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of CC Chemokine Receptor 2A in Complex with an Orthosteric Antagonist Provides Insights for the Design of Selective Antagonists.

Apel, A.K.Cheng, R.K.Y.Tautermann, C.S.Brauchle, M.Huang, C.Y.Pautsch, A.Hennig, M.Nar, H.Schnapp, G.

(2019) Structure 27: 427-438.e5

  • DOI: 10.1016/j.str.2018.10.027
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We determined two crystal structures of the chemokine receptor CCR2A in complex with the orthosteric antagonist MK-0812. Full-length CCR2A, stabilized by rubredoxin and a series of five mutations were resolved at 3.3 Å. An N- and C-terminally truncat ...

    We determined two crystal structures of the chemokine receptor CCR2A in complex with the orthosteric antagonist MK-0812. Full-length CCR2A, stabilized by rubredoxin and a series of five mutations were resolved at 3.3 Å. An N- and C-terminally truncated CCR2A construct was crystallized in an alternate crystal form, which yielded a 2.7 Å resolution structure using serial synchrotron crystallography. Our structures provide a clear structural explanation for the observed key role of residue E291 7.39 in high-affinity binding of several orthosteric CCR2 antagonists. By combining all the structural information collected, we generated models of co-structures for the structurally diverse pyrimidine amide class of CCR2 antagonists. Even though the representative Ex15 overlays well with MK-0812, it also interacts with the non-conserved H121 3.33 , resulting in a significant selectivity over CCR5. Insights derived from this work will facilitate drug discovery efforts directed toward highly selective CCR2 antagonists with potentially superior efficacy.


    Organizational Affiliation

    Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorferstrasse 65, 88397 Biberach, Germany.,Swiss Light Source, Paul Scherrer Institute, 5232 Villigen, Switzerland.,LeadXpro AG, PARK InnovAARE, 5234 Villigen, Switzerland.,Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorferstrasse 65, 88397 Biberach, Germany. Electronic address: gisela.schnapp@boehringer-ingelheim.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-C chemokine receptor type 2,Rubredoxin,C-C chemokine receptor type 2
A, B
349Homo sapiensClostridium pasteurianum
This entity is chimeric
Mutation(s): 0 
Gene Names: CCR2 (CMKBR2),
Find proteins for P41597 (Homo sapiens)
Go to Gene View: CCR2
Go to UniProtKB:  P41597
Find proteins for P00268 (Clostridium pasteurianum)
Go to UniProtKB:  P00268
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, B
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
F7N
Query on F7N

Download SDF File 
Download CCD File 
A, B
[(3~{S},4~{S})-3-methoxyoxan-4-yl]-[(1~{R},3~{S})-3-propan-2-yl-3-[[3-(trifluoromethyl)-7,8-dihydro-5~{H}-1,6-naphthyridin-6-yl]carbonyl]cyclopentyl]azanium
C24 H35 F3 N3 O3
MTMDXAIUENDNDL-RJSMDTJLSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.570α = 90.00
b = 64.550β = 91.19
c = 131.200γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
AutoPROCdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-03-13
    Type: Data collection, Database references