5MT4

COMPLEMENT FACTOR D IN COMPLEX WITH A REVERSIBLE BENZOIC ACID BASED INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Based Library Design and Fragment Screening for the Identification of Reversible Complement Factor D Protease Inhibitors.

Vulpetti, A.Randl, S.Rudisser, S.Ostermann, N.Erbel, P.Mac Sweeney, A.Zoller, T.Salem, B.Gerhartz, B.Cumin, F.Hommel, U.Dalvit, C.Lorthiois, E.Maibaum, J.

(2017) J. Med. Chem. 60: 1946-1958

  • DOI: 10.1021/acs.jmedchem.6b01684
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chronic dysregulation of alternative complement pathway activation has been associated with diverse clinical disorders including age-related macular degeneration and paroxysmal nocturnal hemoglobinurea. Factor D is a trypsin-like serine protease with ...

    Chronic dysregulation of alternative complement pathway activation has been associated with diverse clinical disorders including age-related macular degeneration and paroxysmal nocturnal hemoglobinurea. Factor D is a trypsin-like serine protease with a narrow specificity for arginine in the P1 position, which catalyzes the first enzymatic reaction of the amplification loop of the alternative pathway. In this article, we describe two hit finding approaches leading to the discovery of new chemical matter for this pivotal protease of the complement system: in silico active site mapping for hot spot identification to guide rational structure-based design and NMR screening of focused and diverse fragment libraries. The wealth of information gathered by these complementary approaches enabled the identification of ligands binding to different subpockets of the latent Factor D conformation and was instrumental for understanding the binding requirements for the generation of the first known potent noncovalent reversible Factor D inhibitors.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Complement factor D
A
232Homo sapiensMutation(s): 0 
Gene Names: CFD (DF, PFD)
EC: 3.4.21.46
Find proteins for P00746 (Homo sapiens)
Go to Gene View: CFD
Go to UniProtKB:  P00746
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M7O
Query on M7O

Download SDF File 
Download CCD File 
A
2-[(phenylmethyl)carbamoylamino]benzoic acid
C15 H14 N2 O3
QCLRLHJAKXQKSY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
M7OKd: 500000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.476α = 90.00
b = 50.839β = 104.93
c = 39.366γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references