6ZHO | pdb_00006zho

Crystal structure of a CGRP receptor ectodomain heterodimer with bound high affinity inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.214 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.179 (Depositor) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6ZHO

Ligand Structure Quality Assessment 


This is version 3.3 of the entry. See complete history

Literature

Structure-Based Drug Discovery ofN-((R)-3-(7-Methyl-1H-indazol-5-yl)-1-oxo-1-(((S)-1-oxo-3-(piperidin-4-yl)-1-(4-(pyridin-4-yl)piperazin-1-yl)propan-2-yl)amino)propan-2-yl)-2'-oxo-1',2'-dihydrospiro[piperidine-4,4'-pyrido[2,3-d][1,3]oxazine]-1-carboxamide (HTL22562): A Calcitonin Gene-Related Peptide Receptor Antagonist for Acute Treatment of Migraine.

Bucknell, S.J.Ator, M.A.Brown, A.J.H.Brown, J.Cansfield, A.D.Cansfield, J.E.Christopher, J.A.Congreve, M.Cseke, G.Deflorian, F.Jones, C.R.Mason, J.S.O'Brien, M.A.Ott, G.R.Pickworth, M.Southall, S.M.

(2020) J Med Chem 63: 7906-7920

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01003
  • Primary Citation Related Structures: 
    6ZHO, 6ZIS

  • PubMed Abstract: 

    Structure-based drug design enabled the discovery of 8 , HTL22562, a calcitonin gene-related peptide (CGRP) receptor antagonist. The structure of 8 complexed with the CGRP receptor was determined at a 1.6 Å resolution. Compound 8 is a highly potent, selective, metabolically stable, and soluble compound suitable for a range of administration routes that have the potential to provide rapid systemic exposures with resultant high levels of receptor coverage (e.g., subcutaneous). The low lipophilicity coupled with a low anticipated clinically efficacious plasma exposure for migraine also suggests a reduced potential for hepatotoxicity. These properties have led to 8 being selected as a clinical candidate for acute treatment of migraine.


  • Organizational Affiliation
    • Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, U.K.

Macromolecule Content 

  • Total Structure Weight: 67.85 kDa 
  • Atom Count: 5,282 
  • Modeled Residue Count: 577 
  • Deposited Residue Count: 594 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor594Escherichia coli K-12Homo sapiensMutation(s): 0 
Gene Names: malEb4034JW3994RAMP1CALCRLCGRPR
UniProt & NIH Common Fund Data Resources
Find proteins for O60894 (Homo sapiens)
Explore O60894 
Go to UniProtKB:  O60894
PHAROS:  O60894
GTEx:  ENSG00000132329 
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q16602 (Homo sapiens)
Explore Q16602 
Go to UniProtKB:  Q16602
PHAROS:  Q16602
GTEx:  ENSG00000064989 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9Q16602O60894
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan: G07411ON
GlyCosmos: G07411ON

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QLQ
(Subject of Investigation/LOI)

Query on QLQ



Download:Ideal Coordinates CCD File
C [auth A]~{N}-[(2~{R})-3-(7-methyl-2~{H}-indazol-5-yl)-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-piperidin-4-yl-1-(4-pyridin-4-ylpiperazin-1-yl)propan-2-yl]amino]propan-2-yl]-2-oxidanylidene-spiro[1~{H}-pyrido[2,3-d][1,3]oxazine-4,4'-piperidine]-1'-carboxamide
C40 H49 N11 O5
LIPVCPUZWNTQHV-SAIUNTKASA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.214 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.179 (Depositor) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.725α = 90
b = 76.961β = 90
c = 97.028γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-08-05
    Changes: Database references, Structure summary
  • Version 3.0: 2021-08-18
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 3.1: 2021-08-25
    Changes: Advisory, Database references, Structure summary
  • Version 3.2: 2024-01-24
    Changes: Data collection, Refinement description
  • Version 3.3: 2024-11-13
    Changes: Structure summary