3WD4

Serratia marcescens Chitinase B complexed with azide inhibitor and quinoline compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor

Hirose, T.Maita, N.Gouda, H.Koseki, J.Yamamoto, T.Sugawara, A.Nakano, H.Hirono, S.Shiomi, K.Watanabe, T.Taniguchi, H.Sharpless, K.B.Omura, S.Sunazuka, T.

(2013) Proc.Natl.Acad.Sci.USA 110: 15892-15897

  • DOI: 10.1073/pnas.1315049110
  • Primary Citation of Related Structures:  3WD0, 3WD1, 3WD2, 3WD3

  • PubMed Abstract: 
  • The Huisgen cycloaddition of azides and alkynes, accelerated by target biomolecules, termed "in situ click chemistry," has been successfully exploited to discover highly potent enzyme inhibitors. We have previously reported a specific Serratia marces ...

    The Huisgen cycloaddition of azides and alkynes, accelerated by target biomolecules, termed "in situ click chemistry," has been successfully exploited to discover highly potent enzyme inhibitors. We have previously reported a specific Serratia marcescens chitinase B (SmChiB)-templated syn-triazole inhibitor generated in situ from an azide-bearing inhibitor and an alkyne fragment. Several in situ click chemistry studies have been reported. Although some mechanistic evidence has been obtained, such as X-ray analysis of [protein]-["click ligand"] complexes, indicating that proteins act as both mold and template between unique pairs of azide and alkyne fragments, to date, observations have been based solely on "postclick" structural information. Here, we describe crystal structures of SmChiB complexed with an azide ligand and an O-allyl oxime fragment as a mimic of a click partner, revealing a mechanism for accelerating syn-triazole formation, which allows generation of its own distinct inhibitor. We have also performed density functional theory calculations based on the X-ray structure to explore the acceleration of the Huisgen cycloaddition by SmChiB. The density functional theory calculations reasonably support that SmChiB plays a role by the cage effect during the pretranslation and posttranslation states of selective syn-triazole click formation.


    Organizational Affiliation

    The Kitasato Institute, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, and School of Pharmacy, Kitasato University, Tokyo 108-8641, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chitinase B
A
503Serratia marcescensGene Names: chiB
EC: 3.2.1.14
Find proteins for P11797 (Serratia marcescens)
Go to UniProtKB:  P11797
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
QUB
Query on QUB

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Download CCD File 
A
(E)-N-(prop-2-en-1-yloxy)-1-(quinolin-4-yl)methanimine
C13 H12 N2 O
QNCJWFLSMPZQBD-XNTDXEJSSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
A1L
Query on A1L

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Download CCD File 
A
[2-[[(2S)-1-[bis(phenylmethyl)amino]-5-[[N-(methylcarbamoyl)carbamimidoyl]amino]-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-diazonio-azanide
C24 H31 N9 O3
WCLXSHAWFUUDKF-FQEVSTJZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A1LIC50: 580 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.166 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 97.455α = 90.00
b = 97.455β = 90.00
c = 197.537γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling
ADSCdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-11-06
    Type: Database references, Structure summary