5KMH

Structure of CavAb in complex with Br-verapamil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural basis for inhibition of a voltage-gated Ca(2+) channel by Ca(2+) antagonist drugs.

Tang, L.El-Din, T.M.Swanson, T.M.Pryde, D.C.Scheuer, T.Zheng, N.Catterall, W.A.

(2016) Nature 537: 117-121

  • DOI: 10.1038/nature19102
  • Primary Citation of Related Structures:  
    5KLS, 5KLG, 5KLB, 5KMH, 5KMD, 5KMF

  • PubMed Abstract: 
  • Ca 2+ antagonist drugs are widely used in therapy of cardiovascular disorders. Three chemical classes of drugs bind to three separate, but allosterically interacting, receptor sites on Ca V 1.2 channels, the most prominent voltage-gated Ca 2+ (Ca V ) channel type in myocytes in cardiac and vascular smooth muscle ...

    Ca 2+ antagonist drugs are widely used in therapy of cardiovascular disorders. Three chemical classes of drugs bind to three separate, but allosterically interacting, receptor sites on Ca V 1.2 channels, the most prominent voltage-gated Ca 2+ (Ca V ) channel type in myocytes in cardiac and vascular smooth muscle. The 1,4-dihydropyridines are used primarily for treatment of hypertension and angina pectoris and are thought to act as allosteric modulators of voltage-dependent Ca 2+ channel activation, whereas phenylalkylamines and benzothiazepines are used primarily for treatment of cardiac arrhythmias and are thought to physically block the pore. The structural basis for the different binding, action, and therapeutic uses of these drugs remains unknown. Here we present crystallographic and functional analyses of drug binding to the bacterial homotetrameric model Ca V channel Ca V Ab, which is inhibited by dihydropyridines and phenylalkylamines with nanomolar affinity in a state-dependent manner. The binding site for amlodipine and other dihydropyridines is located on the external, lipid-facing surface of the pore module, positioned at the interface of two subunits. Dihydropyridine binding allosterically induces an asymmetric conformation of the selectivity filter, in which partially dehydrated Ca 2+ interacts directly with one subunit and blocks the pore. In contrast, the phenylalkylamine Br-verapamil binds in the central cavity of the pore on the intracellular side of the selectivity filter, physically blocking the ion-conducting pathway. Structure-based mutations of key amino-acid residues confirm drug binding at both sites. Our results define the structural basis for binding of dihydropyridines and phenylalkylamines at their distinct receptor sites on Ca V channels and offer key insights into their fundamental mechanisms of action and differential therapeutic uses in cardiovascular diseases.


    Organizational Affiliation

    Department of Pharmacology, University of Washington, Seattle, Washington 98195-7280, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ion transport proteinA, B, C, D285Aliarcobacter butzleri RM4018Mutation(s): 0 
Gene Names: Abu_1752
Membrane Entity: Yes 
UniProt
Find proteins for A8EVM5 (Arcobacter butzleri (strain RM4018))
Explore A8EVM5 
Go to UniProtKB:  A8EVM5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MC3 (Subject of Investigation/LOI)
Query on MC3

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], J [auth A], L [auth B], P [auth D], R [auth D]1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
C36 H72 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-N
 Ligand Interaction
PX6 (Subject of Investigation/LOI)
Query on PX6

Download Ideal Coordinates CCD File 
I [auth A], K [auth B], M [auth C], Q [auth D]1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE
C35 H68 O8 P
PORPENFLTBBHSG-MGBGTMOVSA-M
 Ligand Interaction
6U8 (Subject of Investigation/LOI)
Query on 6U8

Download Ideal Coordinates CCD File 
N [auth C](2~{R})-2-(2-bromophenyl)-5-[2-(3,4-dimethoxyphenyl)ethyl-methyl-amino]-2-propan-2-yl-pentanenitrile
C25 H33 Br N2 O2
KXOBUGZMWSPKEA-RUZDIDTESA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], O [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.535α = 90
b = 125.525β = 90
c = 191.96γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01HL112808
National Research Service AwardUnited StatesT32GM008268

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references
  • Version 1.2: 2016-09-14
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence