5DKP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.5 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
  • Primary Citation of Related Structures:  
    5DKP

  • 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 dysregulation of caseinolytic protease (ClpP) ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit
A,
B,
C,
D,
E,
206Neisseria meningitidis MC58Mutation(s): 0 
Gene Names: clpPNMB1312
EC: 3.4.21.92
UniProt
Find proteins for Q9JZ38 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q9JZ38 
Go to UniProtKB:  Q9JZ38
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JZ38
Protein Feature View
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
agonist ADEP A545567synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download Ideal Coordinates CCD File 
AC [auth h],
CC [auth i],
DC [auth j],
EB [auth A],
EC [auth k],
AC [auth h],
CC [auth i],
DC [auth j],
EB [auth A],
EC [auth k],
FB [auth B],
GB [auth C],
GC [auth l],
HB [auth D],
HC [auth m],
IB [auth E],
IC [auth n],
JB [auth F],
KB [auth G],
LB [auth H],
MB [auth I],
NB [auth J],
OB [auth K],
PB [auth L],
QB [auth M],
RB [auth N],
SB [auth a],
TB [auth b],
UB [auth c],
WB [auth d],
XB [auth e],
YB [auth f],
ZB [auth g]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
BC [auth h],
FC [auth k],
VB [auth c]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MAA
Query on MAA
AB [auth 0],
BB [auth 1],
CA [auth O],
CB [auth 2],
DA [auth P],
AB [auth 0],
BB [auth 1],
CA [auth O],
CB [auth 2],
DA [auth P],
DB [auth 3],
EA [auth Q],
FA [auth R],
GA [auth S],
HA [auth T],
IA [auth U],
JA [auth V],
KA [auth W],
LA [auth X],
MA [auth Y],
NA [auth Z],
OA [auth o],
PA [auth p],
QA [auth q],
RA [auth r],
SA [auth s],
TA [auth t],
UA [auth u],
VA [auth v],
WA [auth w],
XA [auth x],
YA [auth y],
ZA [auth z]
L-PEPTIDE LINKINGC4 H9 N O2ALA
MP8
Query on MP8
AB [auth 0],
BB [auth 1],
CA [auth O],
CB [auth 2],
DA [auth P],
AB [auth 0],
BB [auth 1],
CA [auth O],
CB [auth 2],
DA [auth P],
DB [auth 3],
EA [auth Q],
FA [auth R],
GA [auth S],
HA [auth T],
IA [auth U],
JA [auth V],
KA [auth W],
LA [auth X],
MA [auth Y],
NA [auth Z],
OA [auth o],
PA [auth p],
QA [auth q],
RA [auth r],
SA [auth s],
TA [auth t],
UA [auth u],
VA [auth v],
WA [auth w],
XA [auth x],
YA [auth y],
ZA [auth z]
L-PEPTIDE LINKINGC6 H11 N O2PRO
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000503
Query on PRD_000503
AB [auth 0], BB [auth 1], CA [auth 2], CB [auth 3], DA [auth O], DB [auth P], EA [auth Q], FA [auth R], GA [auth S], HA [auth T], IA [auth U], JA [auth V], KA [auth W], LA [auth X], MA [auth Y], NA [auth Z], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth s], TA [auth t], UA [auth u], VA [auth v], WA [auth w], XA [auth x], YA [auth y], ZA [auth z]ADEP1Cyclic depsipeptide / Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.64α = 90
b = 198.85β = 97.81
c = 144.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references, Structure summary
  • Version 1.2: 2016-03-30
    Changes: Other
  • Version 1.3: 2016-04-06
    Changes: Other
  • Version 1.4: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.5: 2020-01-08
    Changes: Author supporting evidence