› 6fut

X-ray diffraction
1.5Å resolution

Complement factor D in complex with the inhibitor (S)-3'-(aminomethyl)-N-(1,2,3,4-tetrahydronaphthalen-1-yl)-[1,1'-biphenyl]-3-carboxamide

Released:
DOI: 10.2210/pdb6fut/pdb
PDB entry 6fut coloured by chain, front view.
PDB entry 6fut coloured by chain, side view.
PDB entry 6fut coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery and Design of First Benzylamine-Based Ligands Binding to an Unlocked Conformation of the Complement Factor D.
Vulpetti A, Ostermann N, Randl S, Yoon T, Mac Sweeney A, Cumin F, Lorthiois E, Rüdisser S, Erbel P, Maibaum J
ACS Med Chem Lett 9 490-495 (2018)
PMID: 29795765

Function and Biology Details

Reaction catalysed: 
Selective cleavage of Arg-|-Lys bond in complement factor B when in complex with complement subcomponent C3b or with cobra venom factor.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133224 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Complement factor D Chain: A
Molecule details ›
Chain: A
Length: 232 amino acids
Theoretical weight: 24.74 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00746 (Residues: 26-253; Coverage: 98%)
Gene names: CFD, DF, PFD
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases

Ligands and Environments

2 bound ligands:
Ligand E82 1 x E82
Ligand SIN 1 x SIN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 46.225Å b: 77.041Å c: 84.898Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.159 0.158 0.184
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Low-molecular weight inhibitors of the alternative complement pathway.
Schubart et al. (2023)
1 more

1 mention without citation

Phenotype-based clustering of glycosylation-related genes by RNAi-mediated gene silencing.
Yamamoto-Hino et al. (2015)