6QMR

Complement factor D in complex with the inhibitor (S)-2-(2-((3'-(1-amino-2-hydroxyethyl)-[1,1'-biphenyl]-3-yl)methoxy)phenyl)acetic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Design, Synthesis, and Preclinical Characterization of Selective Factor D Inhibitors Targeting the Alternative Complement Pathway.

Karki, R.G., Powers, J., Mainolfi, N., Anderson, K., Belanger, D.B., Liu, D., Ji, N., Jendza, K., Gelin, C.F., Mac Sweeney, A., Solovay, C., Delgado, O., Crowley, M., Liao, S.M., Argikar, U.A., Flohr, S., La Bonte, L.R., Lorthiois, E.L., Vulpetti, A., Brown, A., Long, D., Prentiss, M., Gradoux, N., de Erkenez, A., Cumin, F., Adams, C., Jaffee, B., Mogi, M.

(2019) J Med Chem 62: 4656-4668

  • DOI: 10.1021/acs.jmedchem.9b00271
  • Primary Citation of Related Structures:  
    6QMR, 6QMT

  • PubMed Abstract: 

    • Complement factor D (FD), a highly specific S1 serine protease, plays a central role in the amplification of the alternative complement pathway (AP) of the innate immune system. Dysregulation of AP activity predisposes individuals to diverse disorders su ...

    Complement factor D (FD), a highly specific S1 serine protease, plays a central role in the amplification of the alternative complement pathway (AP) of the innate immune system. Dysregulation of AP activity predisposes individuals to diverse disorders such as age-related macular degeneration, atypical hemolytic uremic syndrome, membranoproliferative glomerulonephritis type II, and paroxysmal nocturnal hemoglobinuria. Previously, we have reported the screening efforts and identification of reversible benzylamine-based FD inhibitors (1 and 2) binding to the open active conformation of FD. In continuation of our drug discovery program, we designed compounds applying structure-based approaches to improve interactions with FD and gain selectivity against S1 serine proteases. We report herein the design, synthesis, and medicinal chemistry optimization of the benzylamine series culminating in the discovery of 12, an orally bioavailable and selective FD inhibitor. 12 demonstrated systemic suppression of AP activation in a lipopolysaccharide-induced AP activation model as well as local ocular suppression in intravitreal injection-induced AP activation model in mice expressing human FD.

    Organizational Affiliation: 

    Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Complement factor D A, B, C, D, E, F254Homo sapiensMutation(s): 0 
Gene Names: CFD, DF, PFD
EC: 3.4.21.46
Find proteins for P00746 (Homo sapiens)
Explore P00746 
Go to UniProtKB:  P00746
NIH Common Fund Data Resources
PHAROS:  P00746
GTEx:  ENSG00000197766
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J6T
Query on J6T
Download Ideal Coordinates CCD File 
A, B, C, D, E, F
2-[2-[[3-[3-[(1~{S})-1-azanyl-2-oxidanyl-ethyl]phenyl]phenyl]methoxy]phenyl]ethanoic acid
C23 H23 N O4
XHLXBWRISOPXQB-OAQYLSRUSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
J6TIC50:  12   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.151α = 83.69
b = 66.613β = 64.36
c = 76.377γ = 74.65
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.3: 2019-09-25
    Changes: Data collection