6QZH

Structure of the human CC Chemokine Receptor 7 in complex with the intracellular allosteric antagonist Cmp2105 and the insertion protein Sialidase NanA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Allosteric Ligand Recognition in the Human CC Chemokine Receptor 7.

Jaeger, K.Bruenle, S.Weinert, T.Guba, W.Muehle, J.Miyazaki, T.Weber, M.Furrer, A.Haenggi, N.Tetaz, T.Huang, C.Y.Mattle, D.Vonach, J.M.Gast, A.Kuglstatter, A.Rudolph, M.G.Nogly, P.Benz, J.Dawson, R.J.P.Standfuss, J.

(2019) Cell 178: 1222-1230.e10

  • DOI: https://doi.org/10.1016/j.cell.2019.07.028
  • Primary Citation of Related Structures:  
    6QZH

  • PubMed Abstract: 

    The CC chemokine receptor 7 (CCR7) balances immunity and tolerance by homeostatic trafficking of immune cells. In cancer, CCR7-mediated trafficking leads to lymph node metastasis, suggesting the receptor as a promising therapeutic target. Here, we present the crystal structure of human CCR7 fused to the protein Sialidase NanA by using data up to 2.1 Å resolution. The structure shows the ligand Cmp2105 bound to an intracellular allosteric binding pocket. A sulfonamide group, characteristic for various chemokine receptor ligands, binds to a patch of conserved residues in the Gi protein binding region between transmembrane helix 7 and helix 8. We demonstrate how structural data can be used in combination with a compound repository and automated thermal stability screening to identify and modulate allosteric chemokine receptor antagonists. We detect both novel (CS-1 and CS-2) and clinically relevant (CXCR1-CXCR2 phase-II antagonist Navarixin) CCR7 modulators with implications for multi-target strategies against cancer.


  • Organizational Affiliation

    Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-C chemokine receptor type 7,Sialidase A,C-C chemokine receptor type 7785Homo sapiensStreptococcus pneumoniaeMutation(s): 1 
Gene Names: CCR7CMKBR7EBI1EVI1nanA
EC: 3.2.1.18
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P62576 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore P62576 
Go to UniProtKB:  P62576
Find proteins for P32248 (Homo sapiens)
Explore P32248 
Go to UniProtKB:  P32248
PHAROS:  P32248
GTEx:  ENSG00000126353 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP32248P62576
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JLW
Query on JLW

Download Ideal Coordinates CCD File 
C [auth A]3-[[4-[[(1~{R})-2,2-dimethyl-1-(5-methylfuran-2-yl)propyl]amino]-1,1-bis(oxidanylidene)-1,2,5-thiadiazol-3-yl]amino]-~{N},~{N},6-trimethyl-2-oxidanyl-benzamide
C22 H29 N5 O5 S
MAYXLCLBDVEYAL-SFHVURJKSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
B [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TAR
Query on TAR

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
JLW Binding MOAD:  6QZH Kd: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.124α = 90
b = 128.809β = 90
c = 100.576γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Commission701647
Swiss National Science FoundationSwitzerland31003A_159558

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description