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: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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
  • Structures With Same Primary Citation

  • 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

    From the Dyax Corp., Burlington, Massachusetts 01803, dsexton@dyax.com.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plasma kallikreinA, B241Homo sapiensMutation(s): 4 
Gene Names: KLK3KLKB1KLKB1_HUMAN
EC: 3.4.21.34
Find proteins for P03952 (Homo sapiens)
Explore P03952 
Go to UniProtKB:  P03952
NIH Common Fund Data Resources
PHAROS  P03952
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DX-2930 HEAVY CHAINH, M225Homo sapiensMutation(s): 0 
Find proteins for S6C4R2 (Homo sapiens)
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Go to UniProtKB:  S6C4R2
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DX-2930 LIGHT CHAINL, N213Homo sapiensMutation(s): 0 
Find proteins for Q7Z3Y4 (Homo sapiens)
Explore Q7Z3Y4 
Go to UniProtKB:  Q7Z3Y4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.12α = 90
b = 113.76β = 94.7
c = 89.05γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

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