4OGY

Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inhibition of plasma kallikrein by a highly specific active site blocking antibody.

Kenniston, J.A.Faucette, R.R.Martik, D.Comeau, S.R.Lindberg, A.P.Kopacz, K.J.Conley, G.P.Chen, J.Viswanathan, M.Kastrapeli, N.Cosic, J.Mason, S.DiLeo, M.Abendroth, J.Kuzmic, P.Ladner, R.C.Edwards, T.E.TenHoor, C.Adelman, B.A.Nixon, A.E.Sexton, D.J.

(2014) J.Biol.Chem. 289: 23596-23608

  • DOI: 10.1074/jbc.M114.569061
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Plasma kallikrein (pKal) proteolytically cleaves high molecular weight kininogen to generate the potent vasodilator and the pro-inflammatory peptide, bradykinin. pKal activity is tightly regulated in healthy individuals by the serpin C1-inhibitor, bu ...

    Plasma kallikrein (pKal) proteolytically cleaves high molecular weight kininogen to generate the potent vasodilator and the pro-inflammatory peptide, bradykinin. pKal activity is tightly regulated in healthy individuals by the serpin C1-inhibitor, but individuals with hereditary angioedema (HAE) are deficient in C1-inhibitor and consequently exhibit excessive bradykinin generation that in turn causes debilitating and potentially fatal swelling attacks. To develop a potential therapeutic agent for HAE and other pKal-mediated disorders, we used phage display to discover a fully human IgG1 monoclonal antibody (DX-2930) against pKal. In vitro experiments demonstrated that DX-2930 potently inhibits active pKal (Ki = 0.120 ± 0.005 nM) but does not target either the zymogen (prekallikrein) or any other serine protease tested. These findings are supported by a 2.1-Å resolution crystal structure of pKal complexed to a DX-2930 Fab construct, which establishes that the pKal active site is fully occluded by the antibody. DX-2930 injected subcutaneously into cynomolgus monkeys exhibited a long half-life (t½ ∼ 12.5 days) and blocked high molecular weight kininogen proteolysis in activated plasma in a dose- and time-dependent manner. Furthermore, subcutaneous DX-2930 reduced carrageenan-induced paw edema in rats. A potent and long acting inhibitor of pKal activity could be an effective treatment option for pKal-mediated diseases, such as HAE.


    Organizational Affiliation

    Beryllium, Bainbridge Island, Washington 98110, and.,From the Dyax Corp., Burlington, Massachusetts 01803, dsexton@dyax.com.,From the Dyax Corp., Burlington, Massachusetts 01803.,Biokin, Watertown, Massachusetts 02472.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plasma kallikrein
A, B
241Homo sapiensMutation(s): 4 
Gene Names: KLKB1 (KLK3)
EC: 3.4.21.34
Find proteins for P03952 (Homo sapiens)
Go to Gene View: KLKB1
Go to UniProtKB:  P03952
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DX-2930 HEAVY CHAIN
H, M
225Homo sapiensMutation(s): 0 
Find proteins for S6C4R2 (Homo sapiens)
Go to UniProtKB:  S6C4R2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DX-2930 LIGHT CHAIN
L, N
213Homo sapiensMutation(s): 0 
Find proteins for Q7Z3Y4 (Homo sapiens)
Go to UniProtKB:  Q7Z3Y4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, L
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.120α = 90.00
b = 113.760β = 94.70
c = 89.050γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-09-10
    Type: Database references