6Q9T

Protein-aromatic foldamer complex crystal structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structure Elucidation of Helical Aromatic Foldamer-Protein Complexes with Large Contact Surface Areas.

Reddy, P.S.Langlois d'Estaintot, B.Granier, T.Mackereth, C.D.Fischer, L.Huc, I.

(2019) Chemistry 25: 11042-11047

  • DOI: 10.1002/chem.201902942
  • Primary Citation of Related Structures:  
    6HZX, 6Q9T

  • PubMed Abstract: 
  • The development of large synthetic ligands could be useful to target the sizeable surface areas involved in protein-protein interactions. Herein, we present long helical aromatic oligoamide foldamers bearing proteinogenic side chains that cover up to 450 Å 2 of the human carbonic anhydrase II (HCA) surface ...

    The development of large synthetic ligands could be useful to target the sizeable surface areas involved in protein-protein interactions. Herein, we present long helical aromatic oligoamide foldamers bearing proteinogenic side chains that cover up to 450 Å 2 of the human carbonic anhydrase II (HCA) surface. The foldamers are composed of aminoquinolinecarboxylic acids bearing proteinogenic side chains and of more flexible aminomethyl-pyridinecarboxylic acids that enhance helix handedness dynamics. Crystal structures of HCA-foldamer complexes were obtained with a 9- and a 14-mer both showing extensive protein-foldamer hydrophobic contacts. In addition, foldamer-foldamer interactions seem to be prevalent in the crystal packing, leading to the peculiar formation of an HCA superhelix wound around a rod of stacked foldamers. Solution studies confirm the positioning of the foldamer at the protein surface as well as a dimerization of the complexes.


    Organizational Affiliation

    Department Pharmazie and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 2A259Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
PHAROS:  P00918
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6H0
Query on 6H0

Download Ideal Coordinates CCD File 
C [auth A]~{N}-[[3-(4-formamidobutoxy)phenyl]methyl]-4-sulfamoyl-benzamide
C19 H23 N3 O5 S
ASGCSQAUBAMMLK-UHFFFAOYSA-N
 Ligand Interaction
QVE
Query on QVE

Download Ideal Coordinates CCD File 
I [auth A],
P [auth A]
8-azanyl-4-(2-hydroxy-2-oxoethyloxy)quinoline-2-carboxylic acid
C12 H10 N2 O5
ISBWTKCQKHNORE-UHFFFAOYSA-N
 Ligand Interaction
QUK
Query on QUK

Download Ideal Coordinates CCD File 
G [auth A],
Q [auth A]
8-azanyl-4-(3-azanylpropoxy)quinoline-2-carboxylic acid
C13 H15 N3 O3
QGMHWPPZJKLYHR-UHFFFAOYSA-N
 Ligand Interaction
QUJ
Query on QUJ

Download Ideal Coordinates CCD File 
D [auth A]8-azanyl-4-(2-methylpropoxy)quinoline-2-carboxylic acid
C14 H16 N2 O3
UQMUZAYVJKDBFB-UHFFFAOYSA-N
 Ligand Interaction
QDD
Query on QDD

Download Ideal Coordinates CCD File 
N [auth A]2-(8-azanyl-2-methanoyl-quinolin-4-yl)ethanoic acid
C12 H10 N2 O3
DUFBLPKLVQQBPI-UHFFFAOYSA-N
 Ligand Interaction
QVS
Query on QVS

Download Ideal Coordinates CCD File 
F [auth A],
L [auth A]
8-azanyl-4-oxidanyl-quinoline-2-carboxylic acid
C10 H8 N2 O3
KZBXAHDVCSOKJO-UHFFFAOYSA-N
 Ligand Interaction
ZY9
Query on ZY9

Download Ideal Coordinates CCD File 
E [auth A],
H [auth A],
J [auth A],
K [auth A],
M [auth A],
E [auth A],
H [auth A],
J [auth A],
K [auth A],
M [auth A],
O [auth A]
6-(aminomethyl)pyridine-2-carboxylic acid
C7 H8 N2 O2
KKWKBQBRQWNTPN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.3α = 90
b = 80.96β = 90
c = 45.62γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata 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: 2019-09-18
    Type: Initial release