6B77

Structures of the two-chain human plasma factor XIIa co-crystallized with potent inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structures of human plasma beta-factor XIIa cocrystallized with potent inhibitors.

Dementiev, A.Silva, A.Yee, C.Li, Z.Flavin, M.T.Sham, H.Partridge, J.R.

(2018) Blood Adv 2: 549-558

  • DOI: 10.1182/bloodadvances.2018016337
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Activated factor XIIa (FXIIa) is a serine protease that has received a great deal of interest in recent years as a potential target for the development of new antithrombotics. Despite the strong interest in obtaining structural information, only the ...

    Activated factor XIIa (FXIIa) is a serine protease that has received a great deal of interest in recent years as a potential target for the development of new antithrombotics. Despite the strong interest in obtaining structural information, only the structure of the FXIIa catalytic domain in its zymogen conformation is available. In this work, reproducible experimental conditions found for the crystallization of human plasma β-FXIIa and crystal growth optimization have led to determination of the first structure of the active form of the enzyme. Two crystal structures of human plasma β-FXIIa complexed with small molecule inhibitors are presented herein. The first is the noncovalent inhibitor benzamidine. The second is an aminoisoquinoline containing a boronic acid-reactive group that targets the catalytic serine. Both benzamidine and the aminoisoquinoline bind in a canonical fashion typical of synthetic serine protease inhibitors, and the protease domain adopts a typical chymotrypsin-like serine protease active conformation. This novel structural data explains the basis of the FXII activation, provides insights into the enzymatic properties of β-FXIIa, and is a great aid toward the further design of protease inhibitors for human FXIIa.


    Organizational Affiliation

    Global Blood Therapeutics, Inc, South San Francisco, CA.,Shamrock Structures, LLC, Woodridge, IL; and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor XII
A
9Homo sapiensMutation(s): 0 
Gene Names: F12
EC: 3.4.21.38
Find proteins for P00748 (Homo sapiens)
Go to Gene View: F12
Go to UniProtKB:  P00748
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor XII
B
243Homo sapiensMutation(s): 0 
Gene Names: F12
EC: 3.4.21.38
Find proteins for P00748 (Homo sapiens)
Go to Gene View: F12
Go to UniProtKB:  P00748
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

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Download CCD File 
B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CWV
Query on CWV

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Download CCD File 
B
[3-(1-aminoisoquinolin-6-yl)phenyl]boronic acid
C15 H13 B N2 O2
CCUGLTODPQTEBR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.174 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 79.402α = 90.00
b = 79.402β = 90.00
c = 122.246γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release