6JTB

Crystal structure of dipeptidyl peptidase 11 (DPP11) with citrate from Porphyromonas gingivalis (Space)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase.

Sakamoto, Y.Suzuki, Y.Nakamura, A.Watanabe, Y.Sekiya, M.Roppongi, S.Kushibiki, C.Iizuka, I.Tani, O.Sakashita, H.Inaka, K.Tanaka, H.Yamada, M.Ohta, K.Honma, N.Shida, Y.Ogasawara, W.Nakanishi-Matsui, M.Nonaka, T.Gouda, H.Tanaka, N.

(2019) Sci Rep 9: 13587-13587

  • DOI: https://doi.org/10.1038/s41598-019-49984-3
  • Primary Citation of Related Structures:  
    6JTB, 6JTC

  • PubMed Abstract: 
  • Antimicrobial resistance is a global public threat and raises the need for development of new antibiotics with a novel mode of action. The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to a new class of serine peptidases, family S46 ...

    Antimicrobial resistance is a global public threat and raises the need for development of new antibiotics with a novel mode of action. The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to a new class of serine peptidases, family S46. Because S46 peptidases are not found in mammals, these enzymes are attractive targets for novel antibiotics. However, potent and selective inhibitors of these peptidases have not been developed to date. In this study, a high-resolution crystal structure analysis of PgDPP11 using a space-grown crystal enabled us to identify the binding of citrate ion, which could be regarded as a lead fragment mimicking the binding of a substrate peptide with acidic amino acids, in the S1 subsite. The citrate-based pharmacophore was utilized for in silico inhibitor screening. The screening resulted in an active compound SH-5, the first nonpeptidyl inhibitor of S46 peptidases. SH-5 and a lipophilic analog of SH-5 showed a dose-dependent inhibitory effect against the growth of P. gingivalis. The binding mode of SH-5 was confirmed by crystal structure analysis. Thus, these compounds could be lead structures for the development of selective inhibitors of PgDPP11.


    Organizational Affiliation

    Center for Molecular Analysis, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan. ntanaka@pharm.showa-u.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Asp/Glu-specific dipeptidyl-peptidase720Porphyromonas gingivalis ATCC 33277Mutation(s): 0 
Gene Names: dpp11PGN_0607
EC: 3.4.14
UniProt
Find proteins for B2RID1 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
Explore B2RID1 
Go to UniProtKB:  B2RID1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2RID1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.13α = 90
b = 103.35β = 90
c = 176.52γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata scaling
xia2data reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan25462872
Japan Society for the Promotion of ScienceJapan16K08322
Japan Society for the Promotion of ScienceJapan18K06629
Japan Society for the Promotion of ScienceJapan18K06661
Japan Society for the Promotion of ScienceJapan17H03790
Japan Society for the Promotion of ScienceJapan16H04902
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanH29-A3
Japan Agency for Medical Research and Development (AMED)JapanBINDS 0026
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanCR1405-CR1905

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release