5DKP

Crystal Structure of N. meningitidis ClpP in complex with agonist ADEP A54556.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.381 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Development and Characterization of Potent Cyclic Acyldepsipeptide Analogues with Increased Antimicrobial Activity.

Goodreid, J.D.Janetzko, J.Santa Maria, J.P.Wong, K.S.Leung, E.Eger, B.T.Bryson, S.Pai, E.F.Gray-Owen, S.D.Walker, S.Houry, W.A.Batey, R.A.

(2016) J.Med.Chem. 59: 624-646

  • DOI: 10.1021/acs.jmedchem.5b01451

  • PubMed Abstract: 
  • The problem of antibiotic resistance has prompted the search for new antibiotics with novel mechanisms of action. Analogues of the A54556 cyclic acyldepsipeptides (ADEPs) represent an attractive class of antimicrobial agents that act through dysregul ...

    The problem of antibiotic resistance has prompted the search for new antibiotics with novel mechanisms of action. Analogues of the A54556 cyclic acyldepsipeptides (ADEPs) represent an attractive class of antimicrobial agents that act through dysregulation of caseinolytic protease (ClpP). Previous studies have shown that ADEPs are active against Gram-positive bacteria (e.g., MRSA, VRE, PRSP (penicillin-resistant Streptococcus pneumoniae)); however, there are currently few studies examining Gram-negative bacteria. In this study, the synthesis and biological evaluation of 14 novel ADEPs against a variety of pathogenic Gram-negative and Gram-positive organisms is outlined. Optimization of the macrocyclic core residues and N-acyl side chain culminated in the development of 26, which shows potent activity against the Gram-negative species Neisseria meningitidis and Neisseria gonorrheae and improved activity against the Gram-positive organisms Staphylococcus aureus and Enterococcus faecalis in comparison with known analogues. In addition, the co-crystal structure of an ADEP-ClpP complex derived from N. meningitidis was solved.


    Organizational Affiliation

    Davenport Research Laboratories, Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent Clp protease proteolytic subunit
A, B, C, D, E, F, G, H, I, J, K, L, M, N, a, b, c, d, e, f, g, h, i, j, k, l, m, n
206Neisseria meningitidis serogroup B (strain MC58)Mutation(s): 0 
Gene Names: clpP
EC: 3.4.21.92
Find proteins for Q9JZ38 (Neisseria meningitidis serogroup B (strain MC58))
Go to UniProtKB:  Q9JZ38
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
agonist ADEP A54556
O, P, Q, R, S, T, U, V, W, X, Y, Z, o, p, q, r, s, t, u, v, w, x, y, z, 0, 1, 2, 3
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
a, A, b, B, c, C, d, D, e, E, f, F, G, g, H, h, I, i, J, j, K, k, L, l, M, m, N, n
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
c, h, k
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000503
Query on PRD_000503
0,1,2,3,o,O,p,P,q,Q,R,r,S,s,T,t,u,U,V,v,W,w,X,x,Y,y,Z,zADEP1Cyclic depsipeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.381 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 117.640α = 90.00
b = 198.850β = 97.81
c = 144.040γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
SCALAdata scaling
MOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (Canada)CanadaMOP-130374
CIHR Institute of Infection and ImmunityCanadaXNE-86945

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-10
    Type: Database references, Structure summary
  • Version 1.2: 2016-03-30
    Type: Other
  • Version 1.3: 2016-04-06
    Type: Other
  • Version 1.4: 2017-09-20
    Type: Author supporting evidence, Derived calculations