Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.17 kDa 
• Atom Count: 1972 
• Residue Count: 230 
• Unique protein chains: 1

5MT0

COMPLEMENT FACTOR D IN COMPLEX WITH A REVERSIBLE INDOLE CARBOXYLIC ACID BASED INHIBITOR

• DOI: 10.2210/pdb5MT0/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-01-06 Released: 2017-02-15 
• Deposition Author(s): Mac Sweeney, A., Ostermann, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.196 
• R-Value Work: 0.154 

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

• PubMed: 28157311 
• DOI: 10.1021/acs.jmedchem.6b01684
• Primary Citation of Related Structures:  
  5MT0, 5MT4


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement factor D	A	232	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QJS	A	5-fluoranyl-3-[[(1~{S},2~{S})-2-phenylcyclopropyl]carbonylamino]-1~{H}-indole-2-carboxylic acid C19 H15 F N2 O3 LBCNHUJFDVBZDB-OLZOCXBDSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
QJS	Kd:  500000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.196 
• R-Value Work: 0.154 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.477	α = 90
b = 49.527	β = 106.36
c = 39.263	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-01-06 
• Released Date: 2017-02-15 
Deposition Author(s): Mac Sweeney, A., Ostermann, N.

Revision History 

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2017-03-22
  Changes: Database references
• Version 1.2: 2019-02-20
  Changes: Advisory, Data collection, Derived calculations