5NAR

Complement factor D in complex with the inhibitor (S)-pyrrolidine-1,2-dicarboxylic acid 1-[(1-carbamoyl-1H-indol-3-yl)-amide] 2-[(3-trifluoromethoxy-phenyl)-amide]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of Highly Potent and Selective Small-Molecule Reversible Factor D Inhibitors Demonstrating Alternative Complement Pathway Inhibition in Vivo.

Lorthiois, E.Anderson, K.Vulpetti, A.Rogel, O.Cumin, F.Ostermann, N.Steinbacher, S.Mac Sweeney, A.Delgado, O.Liao, S.M.Randl, S.Rudisser, S.Dussauge, S.Fettis, K.Kieffer, L.de Erkenez, A.Yang, L.Hartwieg, C.Argikar, U.A.La Bonte, L.R.Newton, R.Kansara, V.Flohr, S.Hommel, U.Jaffee, B.Maibaum, J.

(2017) J Med Chem 60: 5717-5735

  • DOI: 10.1021/acs.jmedchem.7b00425
  • Primary Citation of Related Structures:  
    5NBA, 5NAR, 5NB6, 5NAT, 5NAW, 5NB7

  • PubMed Abstract: 
  • The highly specific S1 serine protease factor D (FD) plays a central role in the amplification of the complement alternative pathway (AP) of the innate immune system. Genetic associations in humans have implicated AP activation in age-related macular deg ...

    The highly specific S1 serine protease factor D (FD) plays a central role in the amplification of the complement alternative pathway (AP) of the innate immune system. Genetic associations in humans have implicated AP activation in age-related macular degeneration (AMD), and AP dysfunction predisposes individuals to disorders such as paroxysmal nocturnal hemoglobinuria (PNH) and atypical hemolytic uremic syndrome (aHUS). The combination of structure-based hit identification and subsequent optimization of the center (S)-proline-based lead 7 has led to the discovery of noncovalent reversible and selective human factor D (FD) inhibitors with drug-like properties. The orally bioavailable compound 2 exerted excellent potency in 50% human whole blood in vitro and blocked AP activity ex vivo after oral administration to monkeys as demonstrated by inhibition of membrane attack complex (MAC) formation. Inhibitor 2 demonstrated sustained oral and ocular efficacy in a model of lipopolysaccharide (LPS)-induced systemic AP activation in mice expressing human FD.


    Organizational Affiliation

    Novartis Pharma AG, Novartis Institutes for BioMedical Research , Novartis Campus, CH-4056 Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Complement factor D A232Homo sapiensMutation(s): 0 
Gene Names: CFDDFPFD
EC: 3.4.21.46
Find proteins for P00746 (Homo sapiens)
Explore P00746 
Go to UniProtKB:  P00746
NIH Common Fund Data Resources
PHAROS:  P00746
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8RW
Query on 8RW

Download Ideal Coordinates CCD File 
A
(2~{S})-~{N}1-(1-aminocarbonylindol-3-yl)-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide
C22 H20 F3 N5 O4
GPEWMCZCFCZAEI-SFHVURJKSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8RWIC50:  500   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.159 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.802α = 90
b = 44.516β = 117.69
c = 63.744γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Database references