5NB7

Complement factor D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.143 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acs.jmedchem.7b00425
  • Primary Citation of Related Structures:  
    5NAR, 5NAT, 5NAW, 5NB6, 5NB7, 5NBA

  • 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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement factor D230Homo sapiensMutation(s): 0 
Gene Names: CFDDFPFD
EC: 3.4.21.46
UniProt & NIH Common Fund Data Resources
Find proteins for P00746 (Homo sapiens)
Explore P00746 
Go to UniProtKB:  P00746
PHAROS:  P00746
GTEx:  ENSG00000197766 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00746
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8NQ
Query on 8NQ

Download Ideal Coordinates CCD File 
D [auth A]1-[2-[(1~{R},3~{S},5~{R})-3-[(6-bromanylpyridin-2-yl)carbamoyl]-2-azabicyclo[3.1.0]hexan-2-yl]-2-oxidanylidene-ethyl]indazole-3-carboxamide
C21 H19 Br N6 O3
CWZUTHDJLNZLCM-DFBGVHRSSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
8NQ BindingDB:  5NB7 IC50: min: 5, max: 20 (nM) from 5 assay(s)
Binding MOAD:  5NB7 IC50: 6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.143 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.801α = 90
b = 49.884β = 106.08
c = 39.088γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description