5NCQ | pdb_00005ncq

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

• PDB DOI: https://doi.org/10.2210/pdb5NCQ/pdb

• Classification: HYDROLASE
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2017-03-06 Released: 2018-01-10 
• Deposition Author(s): Bublitz, M., Kjellerup, L., O'Hanlon Cohrt, K., Gordon, S., Mortensen, A.L., Clausen, J.D., Pallin, D., Hansen, J.B., Brown, W.D., Fuglsang, A., Winther, A.-M.L.
• Funding Organization(s): Wellcome Trust, Innovation Fund Denmark, Novo Seeds, Boehringer Ingelheim Venture Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.267 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

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

• PubMed: 29293507 
• DOI: https://doi.org/10.1371/journal.pone.0188620
• Primary Citation Related Structures: 
  5NCQ


• 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 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.

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Organizational Affiliation: 
• Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
Pcovery, Copenhagen N, Denmark.
Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
Charles River Laboratories, Harlow, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 112.37 kDa 
• Atom Count: 7,765 
• Modeled Residue Count: 984 
• Deposited Residue Count: 994 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1	A	994	Oryctolagus cuniculus	Mutation(s): 0  EC: 3.6.3.8 (PDB Primary Data), 7.2.2.10 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P04191 (Oryctolagus cuniculus) Explore P04191  Go to UniProtKB:  P04191

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PCW	D [auth A], E [auth A]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H85 N O8 P SNKAWJBJQDLSFF-NVKMUCNASA-O
128	B [auth A]	SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE C16 H16 N8 O19 P3 LQZBDVDATBCNNN-UHEGPQQHSA-N
8T8	F [auth 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
K	C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.267 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.62	α = 90
b = 224.63	β = 90
c = 57.05	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-10 
Deposition Author(s): Bublitz, M., Kjellerup, L., O'Hanlon Cohrt, K., Gordon, S., Mortensen, A.L., Clausen, J.D., Pallin, D., Hansen, J.B., Brown, W.D., Fuglsang, A., Winther, A.-M.L.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	100480/Z/12
Innovation Fund Denmark	Denmark	4019-00019B
Innovation Fund Denmark	Denmark	012-2011-5
Novo Seeds	Denmark	--
Boehringer Ingelheim Venture Fund	Germany	--

Revision History  

• Version 1.0: 2018-01-10
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2026-04-15
  Changes: Data collection, Non-polymer description, Structure summary