6JUH

structure of CavAb in complex with efonidipine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural basis for efonidipine block of a voltage-gated Ca2+channel.

Xu, F.Xiong, W.Huang, Y.Shen, J.Zhou, D.Tang, L.

(2019) Biochem Biophys Res Commun 513: 631-634

  • DOI: https://doi.org/10.1016/j.bbrc.2019.03.176
  • Primary Citation of Related Structures:  
    6JUH

  • PubMed Abstract: 

    Efonidipine is a dual L-/T- type calcium channel blocker with a slow onset of action and a long lasting effect that exibihits antihypertensive and nephroprotective effects. differs from most other DHPs which can induce reflex tachycardia. Efonidipine reduces blood pressure without decreasing cardiac output and exerts organ-protective effects on the heart and kidney. In order to investigate how efonidipine block voltage-gated Ca 2+ channel, we determined the crystal structure of Ca V Ab in complex with efonidipine at atomic resolution using x-ray crystallography. Our results reveal that efonidipine targets the central cavity of a model voltage-gated calcium channel underneath its selectivity filter and occlude the channel in an inactivated state. Binding of efonidipine does not break down the fourfold symmetry of the quaternary structure and its pore structure. Our work provides the structural basis for efonidipine block of a voltage-gated Ca 2+ channel at the molecular level.


  • Organizational Affiliation

    Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, 61004, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ion transport protein
A, B, C, D
267Aliarcobacter butzleri RM4018Mutation(s): 3 
Membrane Entity: Yes 
UniProt
Find proteins for A8EVM5 (Aliarcobacter butzleri (strain RM4018))
Explore A8EVM5 
Go to UniProtKB:  A8EVM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8EVM5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PX4
Query on PX4

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth C],
N [auth C]
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
MC3
Query on MC3

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
R [auth D]
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
C36 H72 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-N
C9X
Query on C9X

Download Ideal Coordinates CCD File 
Q [auth D]2-[phenyl-(phenylmethyl)amino]ethyl (4~{R})-5-(5,5-dimethyl-2-oxidanylidene-1,3,2$l^{5}-dioxaphosphinan-2-yl)-2,6-dimethyl-4-(3-nitrophenyl)-1,4-dihydropyridine-3-carboxylate
C34 H38 N3 O7 P
NSVFSAJIGAJDMR-WJOKGBTCSA-N
G3P
Query on G3P

Download Ideal Coordinates CCD File 
G [auth A],
O [auth C],
P [auth C],
S [auth D]
SN-GLYCEROL-3-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-GSVOUGTGSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth B],
K [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.86α = 90
b = 125.52β = 90
c = 191.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description