5NCQ

Structure of the (SR) Ca2+-ATPase bound to a Tetrahydrocarbazole and TNP-ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Tetrahydrocarbazoles are a novel class of potent P-type ATPase inhibitors with antifungal activity.

Bublitz, M.Kjellerup, L.Cohrt, K.O.Gordon, S.Mortensen, A.L.Clausen, J.D.Pallin, T.D.Hansen, J.B.Fuglsang, A.T.Dalby-Brown, W.Winther, A.L.

(2018) PLoS ONE 13: e0188620-e0188620

  • DOI: 10.1371/journal.pone.0188620

  • PubMed Abstract: 
  • We have identified a series of tetrahydrocarbazoles as novel P-type ATPase inhibitors. Using a set of rationally designed analogues, we have analyzed their structure-activity relationship using functional assays, crystallographic data and computation ...

    We have identified a series of tetrahydrocarbazoles as novel P-type ATPase inhibitors. Using a set of rationally designed analogues, we have analyzed their structure-activity relationship using functional assays, crystallographic data and computational modeling. We found that tetrahydrocarbazoles inhibit adenosine triphosphate (ATP) hydrolysis of the fungal H+-ATPase, depolarize the fungal plasma membrane and exhibit broad-spectrum antifungal activity. Comparative inhibition studies indicate that many tetrahydrocarbazoles also inhibit the mammalian Ca2+-ATPase (SERCA) and Na+,K+-ATPase with an even higher potency than Pma1. We have located the binding site for this compound class by crystallographic structure determination of a SERCA-tetrahydrocarbazole complex to 3.0 Å resolution, finding that the compound binds to a region above the ion inlet channel of the ATPase. A homology model of the Candida albicans H+-ATPase based on this crystal structure, indicates that the compounds could bind to the same pocket and identifies pocket extensions that could be exploited for selectivity enhancement. The results of this study will aid further optimization towards selective H+-ATPase inhibitors as a new class of antifungal agents.


    Organizational Affiliation

    Department of Biochemistry, University of Oxford, Oxford, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
A
994Oryctolagus cuniculusMutation(s): 0 
Gene Names: ATP2A1
EC: 7.2.2.10
Find proteins for P04191 (Oryctolagus cuniculus)
Go to Gene View: ATP2A1
Go to UniProtKB:  P04191
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
8T8
Query on 8T8

Download SDF File 
Download CCD File 
A
(1~{S})-~{N}-[(4-bromophenyl)methyl]-7-(trifluoromethyloxy)-2,3,4,9-tetrahydro-1~{H}-carbazol-1-amine
C20 H18 Br F3 N2 O
YDUCOWUNUQZJIA-KRWDZBQOSA-N
 Ligand Interaction
128
Query on 128

Download SDF File 
Download CCD File 
A
SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE
C16 H17 N8 O19 P3
XFMMHXLUHKBKQE-UHEGPQQHSA-N
 Ligand Interaction
PCW
Query on PCW

Download SDF File 
Download CCD File 
A
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
(Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 125.620α = 90.00
b = 224.630β = 90.00
c = 57.050γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom100480/Z/12
Innovation Fund DenmarkDenmark4019-00019B
Innovation Fund DenmarkDenmark012-2011-5
Novo SeedsDenmark--
Boehringer Ingelheim Venture FundGermany--

Revision History 

  • Version 1.0: 2018-01-10
    Type: Initial release