4Z2I | pdb_00004z2i

Serratia marcescens Chitinase B complexed with macrolide inhibitor 30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.185 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Creation of Customized Bioactivity within a 14-Membered Macrolide Scaffold: Design, Synthesis, and Biological Evaluation Using a Family-18 Chitinase

Sugawara, A.Maita, N.Gouda, H.Yamamoto, T.Hirose, T.Kimura, S.Saito, Y.Nakano, H.Kasai, T.Nakano, H.Shiomi, K.Hirono, S.Watanabe, T.Taniguchi, H.Omura, S.Sunazuka, T.

(2015) J Med Chem 58: 4984-4997

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b00175
  • Primary Citation Related Structures: 
    4Z2G, 4Z2H, 4Z2I, 4Z2J, 4Z2K, 4Z2L

  • PubMed Abstract: 

    Argifin, a 17-membered pentapeptide, inhibits chitinase. As argifin has properties that render it unsuitable as a drug development candidate, we devised a mechanism to create the structural component of argifin that bestows the chitinase inhibition and introduce it into a 14-membered macrolide scaffold. Here we describe (1) the designed macrolide, which exhibits ∼200-fold more potent chitinase inhibition than argifin, (2) the binding modes of the macrolide with Serratia marcescens chitinase B, and (3) the computed analysis explaining the reason for derivatives displaying increased inhibition compared to argifin, the macrolide aglycone displaying inhibition in a nanomolar range. This promises a class of chitinase inhibitors with novel skeletons, providing innovative insight for drug design and the use of macrolides as adaptable, flexible templates for use in drug discovery research and development.


  • Organizational Affiliation
    • †The Kitasato Institute, Kitasato Institute for Life Sciences and Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan.

Macromolecule Content 

  • Total Structure Weight: 57.82 kDa 
  • Atom Count: 4,468 
  • Modeled Residue Count: 498 
  • Deposited Residue Count: 503 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M6B

Query on M6B



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
(1R,2R,3R,6R,7S,8S,9R,10R,12R,13S,17S)-3-ethyl-2,10-dihydroxy-2,6,8,10,12,15,15,17-octamethyl-5-oxo-9-(prop-2-yn-1-yloxy)-4,14,16-trioxabicyclo[11.3.1]heptadec-7-yl {3-[N'-(methylcarbamoyl)carbamimidamido]propyl}carbamate
C34 H59 N5 O10
DJXCCVYRAMGGTR-CTVLDKPJSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
H [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
PO3

Query on PO3



Download:Ideal Coordinates CCD File
I [auth A]PHOSPHITE ION
O3 P
AQSJGOWTSHOLKH-UHFFFAOYSA-N
MOH

Query on MOH



Download:Ideal Coordinates CCD File
J [auth A]METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.185 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.77α = 90
b = 97.77β = 90
c = 196.11γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-07-08
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary