8WKY | pdb_00008wky

Crystal structure of the Melanocortin-4 Receptor (MC4R) in complex with S25

• PDB DOI: https://doi.org/10.2210/pdb8WKY/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  mpstruc


• Deposited: 2023-09-28 Released: 2024-08-07 
• Deposition Author(s): Gimenez, L.E., Martin, C., Yu, J., Hollanders, C., Hernandez, C., Dahir, N.S., Wu, Y., Yao, D., Han, G.W., Wu, L., Poorten, O.V., Lamouroux, A., Mannes, M., Tourwe, D., Zhao, S., Stevens, R.C., Cone, R.D., Ballet, S.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.267 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Novel Cocrystal Structures of Peptide Antagonists Bound to the Human Melanocortin Receptor 4 Unveil Unexplored Grounds for Structure-Based Drug Design.

Gimenez, L.E., Martin, C., Yu, J., Hollanders, C., Hernandez, C.C., Wu, Y., Yao, D., Han, G.W., Dahir, N.S., Wu, L., Van der Poorten, O., Lamouroux, A., Mannes, M., Zhao, S., Tourwe, D., Stevens, R.C., Cone, R.D., Ballet, S.

(2024) J Med Chem 67: 2690-2711

• PubMed: 38345933 
• DOI: https://doi.org/10.1021/acs.jmedchem.3c01822
• Primary Citation Related Structures: 
  8WKY, 8WKZ


• PubMed Abstract: 
  

  Melanocortin 4 receptor (MC4-R) antagonists are actively sought for treating cancer cachexia. We determined the structures of complexes with PG-934 and SBL-MC-31 . These peptides differ from SHU9119 by substituting His ⁶ with Pro ⁶ and inserting Gly ¹⁰ or Arg ¹⁰ . The structures revealed two subpockets at the TM7-TM1-TM2 domains, separated by N285 ^7.36 . Two peptide series based on the complexed peptides led to an antagonist activity and selectivity SAR study. Most ligands retained the SHU9119 potency, but several SBL-MC-31 -derived peptides significantly enhanced MC4-R selectivity over MC1-R by 60- to 132-fold. We also investigated MC4-R coupling to the K ⁺ channel, Kir7.1. Some peptides activated the channel, whereas others induced channel closure independently of G protein coupling. In cell culture studies, channel activation correlated with increased feeding, while a peptide with Kir7.1 inhibitory activity reduced eating. These results highlight the potential for targeting the MC4-R:Kir7.1 complex for treating positive and restrictive eating disorders.

---

Organizational Affiliation: 
• Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.
Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels B-1050, Belgium.
iHuman Institute, ShanghaiTech University, Ren Building, 393 Middle Huaxia Road, Pudong, Shanghai 201210, China.
Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California 90089, United States.
Department of Molecular and Integrative Physiology, School of Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States.
Department of Molecular, Cellular, and Developmental Biology, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, Michigan 48109, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 63.03 kDa 
• Atom Count: 3,787 
• Modeled Residue Count: 478 
• Deposited Residue Count: 545 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Melanocortin receptor 4	A	535	Homo sapiens	Mutation(s): 5  Gene Names: MC4R Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P32245 (Homo sapiens) Explore P32245  Go to UniProtKB:  P32245
PHAROS:  P32245 GTEx:  ENSG00000166603
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V2J8  Go to UniProtKB:  Q9V2J8
UniProt Groups	Q9V2J8P32245

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N-(2-aminoethyl)-5-(2-{[4-(morpholin-4-yl)pyridin-2-yl]amino}-1,3-thiazol-5-yl)pyridine-3-carboxamide	B	10	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLA	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YCM	A	L-PEPTIDE LINKING	C5 H10 N2 O3 S		CYS
4J2	B	D-PEPTIDE LINKING	C13 H13 N O2		--
NLE	B	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.267 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.92	α = 90
b = 44.9	β = 97.74
c = 89.81	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Gimenez, L.E., Martin, C., Yu, J., Hollanders, C., Hernandez, C., Dahir, N.S., Wu, Y., Yao, D., Han, G.W., Wu, L., Poorten, O.V., Lamouroux, A., Mannes, M., Tourwe, D., Zhao, S., Stevens, R.C., Cone, R.D., Ballet, S.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release