8AYH | pdb_00008ayh

Structure of Complement C5 in Complex with small molecule inhibitor and CVF

• PDB DOI: https://doi.org/10.2210/pdb8AYH/pdb
• Entry: 8AYH supersedes: 6I2X
• EM Map EMD-15713: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Naja kaouthia
• Mutation(s): No 


• Deposited: 2022-09-02 Released: 2022-12-21 
• Deposition Author(s): Srinivas, H.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A small-molecule inhibitor of C5 complement protein.

Jendza, K., Kato, M., Salcius, M., Srinivas, H., De Erkenez, A., Nguyen, A., McLaughlin, D., Be, C., Wiesmann, C., Murphy, J., Bolduc, P., Mogi, M., Duca, J., Namil, A., Capparelli, M., Darsigny, V., Meredith, E., Tichkule, R., Ferrara, L., Heyder, J., Liu, F., Horton, P.A., Romanowski, M.J., Schirle, M., Mainolfi, N., Anderson, K., Michaud, G.A.

(2019) Nat Chem Biol 15: 666-668

• PubMed: 31209353 
• DOI: https://doi.org/10.1038/s41589-019-0303-9
• Primary Citation Related Structures: 
  8AYH


• PubMed Abstract: 
  

  The complement pathway is an important part of the immune system, and uncontrolled activation is implicated in many diseases. The human complement component 5 protein (C5) is a validated drug target within the complement pathway, as an anti-C5 antibody (Soliris) is an approved therapy for paroxysmal nocturnal hemoglobinuria. Here, we report the identification, optimization and mechanism of action for the first small-molecule inhibitor of C5 complement protein.

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Organizational Affiliation: 
• Global Discovery Chemistry, Novartis Institutes of Biomedical Research, Cambridge, MA, USA.
Chemical Biology and Therapeutics, Novartis Institutes of Biomedical Research, Cambridge, MA, USA.
Chemical Biology and Therapeutics, Novartis Institutes of Biomedical Research, Basel, Switzerland.
Ophthalmology, Novartis Institutes of Biomedical Research, Cambridge, MA, USA.
Chemical Biology and Therapeutics, Novartis Institutes of Biomedical Research, Cambridge, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 371.45 kDa 
• Atom Count: 19,109 
• Modeled Residue Count: 2,414 
• Deposited Residue Count: 3,298 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C5 beta chain	A [auth C]	657	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01031 (Homo sapiens) Explore P01031  Go to UniProtKB:  P01031
PHAROS:  P01031 GTEx:  ENSG00000106804

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C5 alpha chain	B [auth A]	999	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01031 (Homo sapiens) Explore P01031  Go to UniProtKB:  P01031
PHAROS:  P01031 GTEx:  ENSG00000106804

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobra venom factor	C [auth B]	1,642	Naja kaouthia	Mutation(s): 0
UniProt
Find proteins for Q91132 (Naja kaouthia) Explore Q91132  Go to UniProtKB:  Q91132

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H1H (Subject of Investigation/LOI)	D [auth A]	5-methoxy-2-[[(1~{S})-1-(2-methoxyphenyl)ethyl]carbamoylamino]-4-(4-methylpentoxy)benzoic acid C24 H32 N2 O6 UFAFCKVYKJIJTR-INIZCTEOSA-N
MG	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-21 
Deposition Author(s): Srinivas, H.
• This entry supersedes: 6I2X

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Funding Organization	Location	Grant Number
Other private	Switzerland	--

Revision History  

• Version 1.0: 2022-12-21
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Structure summary