1ZMJ

Crystal Structure of the Catalytic Domain of Factor XI in complex with 4-(guanidinomethyl)-phenylboronic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Synthesis and in vitro biological evaluation of aryl boronic acids as potential inhibitors of factor XIa.

Lazarova, T.I.Jin, L.Rynkiewicz, M.Gorga, J.C.Bibbins, F.Meyers, H.V.Babine, R.Strickler, J.

(2006) Bioorg Med Chem Lett 16: 5022-5027

  • DOI: 10.1016/j.bmcl.2006.07.043
  • Primary Citation of Related Structures:  
    1ZLR, 1ZMJ, 1ZMN, 1ZML

  • PubMed Abstract: 
  • A series of functionalized aryl boronic acids were synthesized and evaluated as potential inhibitors of factor XIa. Crystal structures of the protein-inhibitor complexes led to the design and synthesis of second generation compounds showing single digit micromolar inhibition against FXIa and selectivity against thrombin, trypsin, and FXa ...

    A series of functionalized aryl boronic acids were synthesized and evaluated as potential inhibitors of factor XIa. Crystal structures of the protein-inhibitor complexes led to the design and synthesis of second generation compounds showing single digit micromolar inhibition against FXIa and selectivity against thrombin, trypsin, and FXa.


    Organizational Affiliation

    Medicinal Chemistry, Daiichi Asubio Medical Research Laboratories, LLC, One Kendall Square, Building 700, Cambridge, MA 02139, USA. tlazarova@medchempartners.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor XIA238Homo sapiensMutation(s): 4 
Gene Names: F11
EC: 3.4.21.27
Find proteins for P03951 (Homo sapiens)
Explore P03951 
Go to UniProtKB:  P03951
NIH Common Fund Data Resources
PHAROS:  P03951
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HDB
Query on HDB

Download Ideal Coordinates CCD File 
D [auth A](R)-1-(4-(4-(HYDROXYMETHYL)-1,3,2-DIOXABOROLAN-2-YL)BENZYL)GUANIDINE
C11 H16 B N3 O3
IIZOWFNBOXPJES-SNVBAGLBSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
E [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.201 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.775α = 90
b = 120.775β = 90
c = 120.775γ = 90
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Data collection