3WD1

Serratia marcescens Chitinase B complexed with syn-triazole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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 U S A 110: 15892-15897

  • DOI: https://doi.org/10.1073/pnas.1315049110
  • Primary Citation of Related Structures:  
    3WD0, 3WD1, 3WD2, 3WD3, 3WD4

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitinase B503Serratia marcescensMutation(s): 0 
Gene Names: chiB
EC: 3.2.1.14
UniProt
Find proteins for P11797 (Serratia marcescens)
Explore P11797 
Go to UniProtKB:  P11797
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11797
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ST7
Query on ST7

Download Ideal Coordinates CCD File 
O [auth A]N,N-dibenzyl-N~5~-[N-(methylcarbamoyl)carbamimidoyl]-N~2~-{[5-({[(E)-(quinolin-4-ylmethylidene)amino]oxy}methyl)-1H-1,2,3-triazol-1-yl]acetyl}-L-ornithinamide
C37 H41 N11 O4
YASCYEPUKAYRJI-IPZIAFNWSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
PO3
Query on PO3

Download Ideal Coordinates CCD File 
N [auth A]PHOSPHITE ION
O3 P
AQSJGOWTSHOLKH-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ST7 Binding MOAD:  3WD1 IC50: 22 (nM) from 1 assay(s)
PDBBind:  3WD1 IC50: 22 (nM) from 1 assay(s)
BindingDB:  3WD1 IC50: 22 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.768α = 90
b = 97.768β = 90
c = 197.757γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-11-06
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description