8AX5

Crystal structure of a CGRP receptor ectodomain heterodimer bound to macrocyclic inhibitor HTL0029881

• PDB DOI: https://doi.org/10.2210/pdb8AX5/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2022-08-30 Released: 2022-12-07 
• Deposition Author(s): Southall, S.M., Watson, S.P.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.277 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 

Starting Model: experimental

Literature

Novel Macrocyclic Antagonists of the CGRP Receptor Part 2: Stereochemical Inversion Induces an Unprecedented Binding Mode.

Southall, S.M., Banerjee, J., Brown, J., Butkovic, K., Cansfield, A.D., Cansfield, J.E., Congreve, M.S., Cseke, G., Deflorian, F., Hunjadi, M.P., Hutinec, A., Inturi, T.K., Rupcic, R., Saxty, G., Watson, S.P.

(2022) ACS Med Chem Lett 13: 1776-1782

• PubMed: 36385934 
• DOI: https://doi.org/10.1021/acsmedchemlett.2c00400
• Primary Citation of Related Structures:  
  8AX5, 8AX6, 8AX7


• PubMed Abstract: 
  

  The diastereomeric macrocyclic calcitonin gene-related peptide (CGRP) antagonists HTL0029881 ( 3 ) and HTL0029882 ( 4 ), in which the stereochemistry of a spiro center is reversed, surprisingly demonstrate comparable potency. X-ray crystallographic characterization demonstrates that 3 binds to the CGRP receptor in a precedented manner but that 4 binds in an unprecedented, unexpected, and radically different manner. The observation of this phenomenon is noteworthy and may open novel avenues for CGRP receptor antagonist design.

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Organizational Affiliation: 

Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 67.45 kDa 
• Atom Count: 4,522 
• Modelled Residue Count: 549 
• Deposited Residue Count: 593 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor	A	593	Escherichia coli K-12, Homo sapiens	Mutation(s): 0  Gene Names: malE, b4034, JW3994, RAMP1, CALCRL, CGRPR
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for O60894 (Homo sapiens) Explore O60894  Go to UniProtKB:  O60894
PHAROS:  O60894 GTEx:  ENSG00000132329
Find proteins for Q16602 (Homo sapiens) Explore Q16602  Go to UniProtKB:  Q16602
PHAROS:  Q16602 GTEx:  ENSG00000064989
UniProt Groups	P0AEX9Q16602O60894

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B [auth C]	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OKU (Subject of Investigation/LOI)	C [auth A]	(1~{R},10~{R},20~{E})-12-methyl-10-[(7-methyl-2~{H}-indazol-5-yl)methyl]-15,18-dioxa-9,12,24,26-tetrazapentacyclo[20.5.2.1^{1,4}.1^{3,7}.0^{25,28}]hentriaconta-3,5,7(30),20,22,24,28-heptaene-8,11,27-trione C35 H36 N6 O5 LJMGRDULDLZQAJ-ATKWODBQSA-N
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B [auth C]	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.277 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.687	α = 90
b = 78.534	β = 90
c = 97.926	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-07 
Deposition Author(s): Southall, S.M., Watson, S.P.

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Funding Organization	Location	Grant Number
Not funded	United Kingdom	--

Revision History  

• Version 1.0: 2022-12-07
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary