1ZPB

Crystal Structure of the Catalytic Domain of Coagulation Factor XI in Complex with 4-Methyl-pentanoic acid {1-[4-guanidino-1-(thiazole-2-carbonyl)-butylcarbamoyl]-2-methyl-propyl}-amide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthesis, SAR exploration, and X-ray crystal structures of factor XIa inhibitors containing an alpha-ketothiazole arginine

Deng, H.Bannister, T.D.Jin, L.Babine, R.E.Quinn, J.Nagafuji, P.Celatka, C.A.Lin, J.Lazarova, T.I.Rynkiewicz, M.J.Bibbins, F.Pandey, P.Gorga, J.Meyers, H.V.Abdel-Meguid, S.S.Strickler, J.E.

(2006) Bioorg.Med.Chem.Lett. 16: 3049-3054

  • DOI: 10.1016/j.bmcl.2006.02.052
  • Primary Citation of Related Structures:  1ZPC, 2FDA

  • PubMed Abstract: 
  • Using an alpha-ketothiazole arginine moiety as a key recognition element, a series of small peptidomimetic molecules was designed and synthesized, and their co-crystal structures with factor XIa were studied in an effort to develop smaller, less pept ...

    Using an alpha-ketothiazole arginine moiety as a key recognition element, a series of small peptidomimetic molecules was designed and synthesized, and their co-crystal structures with factor XIa were studied in an effort to develop smaller, less peptidic inhibitors as antithrombotic agents.


    Organizational Affiliation

    Department of Medicinal Chemistry, Daiichi Asubio Medical Research Laboratories, LLC (DAIAMED), One Kendall Square, Bldg 700, Cambridge, MA 02139, USA. hongfeng.deng@praecis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor XI
A
238Homo sapiensGene Names: F11
EC: 3.4.21.27
Find proteins for P03951 (Homo sapiens)
Go to Gene View: F11
Go to UniProtKB:  P03951
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
995
Query on 995

Download SDF File 
Download CCD File 
A
4-METHYL-PENTANOIC ACID {1-[4-GUANIDINO-1-(THIAZOLE-2-CARBONYL)-BUTYLCARBAMOYL]-2-METHYL-PROPYL}-AMIDE
C20 H36 N6 O3 S
ZXELQWLUDMEUHS-HOCLYGCPSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
995IC50: 850 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 121.173α = 90.00
b = 121.173β = 90.00
c = 121.173γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNXphasing
HKL-2000data reduction
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2006-04-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance