6CFD | pdb_00006cfd

ADEP4 bound to E. faecium ClpP

PDB DOI: https://doi.org/10.2210/pdb6CFD/pdb

Classification: HYDROLASE/ANTIBIOTIC
Organism(s): Enterococcus faecium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-02-14 Released: 2018-05-16
Deposition Author(s): Lee, R.E., Griffith, E.C.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.209 (Depositor), 0.213 (DCC)
R-Value Work:
0.175 (Depositor), 0.179 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

In VivoandIn VitroEffects of a ClpP-Activating Antibiotic against Vancomycin-Resistant Enterococci.

Brown Gandt, A., Griffith, E.C., Lister, I.M., Billings, L.L., Han, A., Tangallapally, R., Zhao, Y., Singh, A.P., Lee, R.E., LaFleur, M.D.

(2018) Antimicrob Agents Chemother 62

PubMed: 29784838 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/AAC.00424-18
Primary Citation Related Structures:
6CFD

PubMed Abstract:
Antibiotics with novel bactericidal mechanisms of action are urgently needed. The antibiotic acyldepsipeptide 4 (ADEP4) activates the ClpP protease and causes cells to self-digest. The effects of ADEP4 and ClpP activation have not been characterized sufficiently for the enterococci, which are important pathogens known for high levels of acquired and intrinsic antibiotic resistance. In the present study, ADEP4 was found to be potently active against both Enterococcus faecalis and Enterococcus faecium , with MIC ₉₀s of 0.016 μg/ml and 0.031 μg/ml, respectively. ClpP purified from E. faecium was found to bind ADEP4 in a surface plasmon resonance analysis, and ClpP activation by ADEP4 was demonstrated biochemically with a β-casein digestion assay. In addition, E. faecium ClpP was crystallized in the presence of ADEP4, revealing ADEP4 binding to ClpP in the activated state. These results confirm that the anti-enterococcal activity of ADEP4 occurs through ClpP activation. In killing curve assays, ADEP4 was found to be bactericidal against stationary-phase vancomycin-resistant E. faecalis (VRE) strain V583, and resistance development was prevented when ADEP4 was combined with multiple classes of approved antibiotics. ADEP4 in combination with partnering antibiotics also eradicated mature VRE biofilms within 72 h of treatment. Biofilm killing with ADEP4 antibiotic combinations was superior to that with the clinically used combinations ampicillin-gentamicin and ampicillin-daptomycin. In a murine peritoneal septicemia model, ADEP4 alone was as effective as ampicillin. ADEP4 coadministered with ampicillin was significantly more effective than either drug alone. These data suggest that ClpP-activating antibiotics may be useful for treating enterococcal infections.

Organizational Affiliation

Arietis Pharma, Boston, Massachusetts, USA.

Macromolecule Content

Total Structure Weight: 336.3 kDa
Atom Count: 20,070
Modeled Residue Count: 2,548
Deposited Residue Count: 2,940
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit	A B C D E A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth L], K [auth M], L [auth N], M [auth S], N [auth T]	210	Enterococcus faecium	Mutation(s): 0 Gene Names: clpP, A5804_002055, A5809_001747, A5810_000386, A5814_002098, A5836_000160, A5841_002116, A5860_002409, AS238_05290, AWT83_05460... clpP, A5804_002055, A5809_001747, A5810_000386, A5814_002098, A5836_000160, A5841_002116, A5860_002409, AS238_05290, AWT83_05460, B1P95_10385, B4W81_08585, BK413_10305, BK695_10280, BK696_10275, BTA10_07855, BTA13_11970, BU181_02235, BU182_15300, BU184_14080, BU185_04695, BU186_06175, BU187_13865, BU188_14880, BU189_03420, BU190_07525, BU191_15420, BU192_05390, BU194_04805, CDL00_11615, CKY17_04320, CKY19_04880, CQR37_09710, CQR38_04150, CQR40_12365, CQR41_03640, CQR43_09890, CRM75_14685, CRN03_11890, CS913_12780, CS915_12510, CS916_12510, DTPHA_601708, EFM1CSP_03625, HMPREF3199_00581 EC: 3.4.21.92
UniProt
Find proteins for Q3XX76 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)) Explore Q3XX76 Go to UniProtKB: Q3XX76
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3XX76
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EZA (Subject of Investigation/LOI) Query on EZA Download:Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain EA [auth L] SDF format, chain GA [auth M] SDF format, chain IA [auth N] SDF format, chain KA [auth S] SDF format, chain MA [auth T] SDF format, chain P [auth A] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain W [auth E] SDF format, chain Y [auth F] MOL2 format, chain BA [auth I] MOL2 format, chain EA [auth L] MOL2 format, chain GA [auth M] MOL2 format, chain IA [auth N] MOL2 format, chain KA [auth S] MOL2 format, chain MA [auth T] MOL2 format, chain P [auth A] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Y [auth F] mmCIF format, chain BA [auth I] mmCIF format, chain EA [auth L] mmCIF format, chain GA [auth M] mmCIF format, chain IA [auth N] mmCIF format, chain KA [auth S] mmCIF format, chain MA [auth T] mmCIF format, chain P [auth A] mmCIF format, chain S [auth C] mmCIF format, chain U [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Y [auth F]	BA [auth I] EA [auth L] GA [auth M] IA [auth N] KA [auth S] BA [auth I], EA [auth L], GA [auth M], IA [auth N], KA [auth S], MA [auth T], P [auth A], S [auth C], U [auth D], W [auth E], Y [auth F]	N-[(6aS,12S,15aS,17R,21R,23aS)-17,21-dimethyl-6,11,15,20,23-pentaoxooctadecahydro-2H,6H,11H,15H-pyrido[2,1-i]dipyrrolo[2,1-c:2',1'-l][1,4,7,10,13]oxatetraazacyclohexadecin-12-yl]-3,5-difluoro-Nalpha-[(2E)-hept-2-enoyl]-L-phenylalaninamide C₃₉ H₅₂ F₂ N₆ O₈ BAEUBYUDIYWBPI-AIRHAPKHSA-N		Interactions Focus chain BA [auth I] Focus chain EA [auth L] Focus chain GA [auth M] Focus chain IA [auth N] Focus chain KA [auth S] Focus chain MA [auth T] Focus chain P [auth A] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth I] Focus chain EA [auth L] Focus chain GA [auth M] Focus chain IA [auth N] Focus chain KA [auth S] Focus chain MA [auth T] Focus chain P [auth A] Focus chain S [auth C] Focus chain U [auth D] Focus chain W [auth E] Focus chain Y [auth F]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain CA [auth K] SDF format, chain DA [auth L] SDF format, chain FA [auth M] SDF format, chain HA [auth N] SDF format, chain JA [auth S] SDF format, chain LA [auth T] SDF format, chain O [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain X [auth F] SDF format, chain Z [auth G] MOL2 format, chain AA [auth I] MOL2 format, chain CA [auth K] MOL2 format, chain DA [auth L] MOL2 format, chain FA [auth M] MOL2 format, chain HA [auth N] MOL2 format, chain JA [auth S] MOL2 format, chain LA [auth T] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Z [auth G] mmCIF format, chain AA [auth I] mmCIF format, chain CA [auth K] mmCIF format, chain DA [auth L] mmCIF format, chain FA [auth M] mmCIF format, chain HA [auth N] mmCIF format, chain JA [auth S] mmCIF format, chain LA [auth T] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Z [auth G]	AA [auth I] CA [auth K] DA [auth L] FA [auth M] HA [auth N] AA [auth I], CA [auth K], DA [auth L], FA [auth M], HA [auth N], JA [auth S], LA [auth T], O [auth A], Q [auth B], R [auth C], T [auth D], V [auth E], X [auth F], Z [auth G]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain AA [auth I] Focus chain CA [auth K] Focus chain DA [auth L] Focus chain FA [auth M] Focus chain HA [auth N] Focus chain JA [auth S] Focus chain LA [auth T] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth K] Focus chain DA [auth L] Focus chain FA [auth M] Focus chain HA [auth N] Focus chain JA [auth S] Focus chain LA [auth T] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.209 (Depositor), 0.213 (DCC)
R-Value Work: 0.175 (Depositor), 0.179 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.395	α = 90
b = 202.166	β = 102.69
c = 97.385	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

Lee, R.E.

Griffith, E.C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5R44AI122426-02

Revision History (Full details and data files)

Version 1.0: 2018-05-16
Type: Initial release
Version 1.1: 2018-06-06
Changes: Data collection, Database references
Version 1.2: 2018-08-08
Changes: Data collection, Database references
Version 1.3: 2019-12-11
Changes: Author supporting evidence
Version 1.4: 2023-10-04
Changes: Data collection, Database references, Refinement description

6CFD | pdb_00006cfd

ADEP4 bound to E. faecium ClpP

Literature

In VivoandIn VitroEffects of a ClpP-Activating Antibiotic against Vancomycin-Resistant Enterococci.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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