6GHV

Structure of a DC-SIGN CRD in complex with high affinity glycomimetic.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Enhancing Potency and Selectivity of a DC-SIGN Glycomimetic Ligand by Fragment-Based Design: Structural Basis.

Medve, L.Achilli, S.Guzman-Caldentey, J.Thepaut, M.Senaldi, L.Le Roy, A.Sattin, S.Ebel, C.Vives, C.Martin-Santamaria, S.Bernardi, A.Fieschi, F.

(2019) Chemistry 25: 14659-14668

  • DOI: 10.1002/chem.201903391
  • Primary Citation of Related Structures:  
    6GHV

  • PubMed Abstract: 
  • Chemical modification of pseudo-dimannoside ligands guided by fragment-based design allowed for the exploitation of an ammonium-binding region in the vicinity of the mannose-binding site of DC-SIGN, leading to the synthesis of a glycomimetic antagonist (compound 16) of unprecedented affinity and selectivity against the related lectin langerin ...

    Chemical modification of pseudo-dimannoside ligands guided by fragment-based design allowed for the exploitation of an ammonium-binding region in the vicinity of the mannose-binding site of DC-SIGN, leading to the synthesis of a glycomimetic antagonist (compound 16) of unprecedented affinity and selectivity against the related lectin langerin. Here, the computational design of pseudo-dimannoside derivatives as DC-SIGN ligands, their synthesis, their evaluation as DC-SIGN selective antagonists, the biophysical characterization of the DC-SIGN/16 complex, and the structural basis for the ligand activity are presented. On the way to the characterization of this ligand, an unusual bridging interaction within the crystals shed light on the plasticity and potential secondary binding sites within the DC-SIGN carbohydrate recognition domain.


    Organizational Affiliation

    Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 38044, Grenoble, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CD209 antigenA, B, C, D, E, F155Homo sapiensMutation(s): 0 
Gene Names: CD209CLEC4L
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NNX6 (Homo sapiens)
Explore Q9NNX6 
Go to UniProtKB:  Q9NNX6
PHAROS:  Q9NNX6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EZ8 (Subject of Investigation/LOI)
Query on EZ8

Download Ideal Coordinates CCD File 
AA [auth D], G [auth A], HA [auth E], N [auth B], NA [auth F], T [auth C][1-[(2~{S},3~{S},4~{R},5~{S},6~{R})-2-[(1~{S},2~{S},4~{S},5~{S})-2-(2-chloroethyloxy)-4,5-bis[[4-(hydroxymethyl)phenyl]methylcarbamoyl]cyclohexyl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-1,2,3-triazol-4-yl]methylazanium
C35 H48 Cl N6 O10
BYGZQFCUFRSCML-RWSQSUCKSA-O
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth D] , CA [auth D] , DA [auth D] , H [auth A] , I [auth A] , IA [auth E] , J [auth A] , JA [auth E] , 
BA [auth D],  CA [auth D],  DA [auth D],  H [auth A],  I [auth A],  IA [auth E],  J [auth A],  JA [auth E],  KA [auth E],  O [auth B],  OA [auth F],  P [auth B],  PA [auth F],  Q [auth B],  QA [auth F],  U [auth C],  V [auth C],  W [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
EA [auth D] , FA [auth E] , GA [auth E] , K [auth A] , L [auth A] , LA [auth E] , M [auth A] , MA [auth F] , 
EA [auth D],  FA [auth E],  GA [auth E],  K [auth A],  L [auth A],  LA [auth E],  M [auth A],  MA [auth F],  R [auth B],  RA [auth F],  S [auth B],  X [auth C],  Y [auth C],  Z [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EZ8 Binding MOAD:  6GHV Kd: 5.20e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.612α = 90
b = 57.507β = 118.67
c = 107.247γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionFranceITN 642870

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references