6I2X

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


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3.35 Å

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1038/s41589-019-0303-9
  • Primary Citation of Related Structures:  
    6I2X

  • 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 ...

    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.


    Organizational Affiliation

    Chemical Biology and Therapeutics, Novartis Institutes of Biomedical Research, Cambridge, MA, USA. gregory.michaud@novartis.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C5A [auth C]657Homo sapiensMutation(s): 0 
Gene Names: C5CPAMD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01031 (Homo sapiens)
Explore P01031 
Go to UniProtKB:  P01031
PHAROS:  P01031
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01031
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C5B [auth A]999Homo sapiensMutation(s): 0 
Gene Names: C5CPAMD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01031 (Homo sapiens)
Explore P01031 
Go to UniProtKB:  P01031
PHAROS:  P01031
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01031
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cobra venom factorC [auth B]1,642Naja kaouthiaMutation(s): 0 
UniProt
Find proteins for Q91132 (Naja kaouthia)
Explore Q91132 
Go to UniProtKB:  Q91132
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91132
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H1H
Query on H1H

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3.35 Å
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 258α = 90
b = 258β = 90
c = 258γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2019-06-26 
  • Deposition Author(s): Srinivas, H.

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2021-02-10
    Changes: Source and taxonomy