3IIT

Factor XA in complex with a cis-1,2-diaminocyclohexane derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design, synthesis, and SAR of cis-1,2-diaminocyclohexane derivatives as potent factor Xa inhibitors. Part II: exploration of 6-6 fused rings as alternative S1 moieties.

Yoshikawa, K.Kobayashi, S.Nakamoto, Y.Haginoya, N.Komoriya, S.Yoshino, T.Nagata, T.Mochizuki, A.Watanabe, K.Suzuki, M.Kanno, H.Ohta, T.

(2009) Bioorg.Med.Chem. 17: 8221-8233

  • DOI: 10.1016/j.bmc.2009.10.024

  • PubMed Abstract: 
  • A series of cis-1,2-diaminocyclohexane derivatives possessing a 6-6 fused ring for the S1 moiety were synthesized as novel factor Xa (fXa) inhibitors. The synthesis, structure-activity relationship (SAR), and physicochemical properties are reported h ...

    A series of cis-1,2-diaminocyclohexane derivatives possessing a 6-6 fused ring for the S1 moiety were synthesized as novel factor Xa (fXa) inhibitors. The synthesis, structure-activity relationship (SAR), and physicochemical properties are reported herein, together with the discovery of compound 45c, which has potent anti-fXa activity, good physicochemical properties and pharmacokinetic (PK) profiles, including a reduced negative food effect.


    Organizational Affiliation

    R&D Division, Daiichi Sankyo Co, Ltd, 1-16-13, Kita-Kasai, Tokyo 134-8630, Japan. yoshikawa.kenji.t6@daiichisankyo.co.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Activated factor Xa heavy chain
A
233Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to Gene View: F10
Go to UniProtKB:  P00742
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Factor X light chain
B
54Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to Gene View: F10
Go to UniProtKB:  P00742
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
D14
Query on D14

Download SDF File 
Download CCD File 
A
7-chloro-N-[(1S,2R,4S)-4-(dimethylcarbamoyl)-2-{[(5-methyl-5,6-dihydro-4H-pyrrolo[3,4-d][1,3]thiazol-2-yl)carbonyl]amino}cyclohexyl]isoquinoline-3-carboxamide
C26 H29 Cl N6 O3 S
GZCKMZURFJCTJE-ZYSHUDEJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D14IC50: 9.5 nM (100) BINDINGDB
D14IC50: 9.5 nM BINDINGMOAD
D14IC50: 9.5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.055α = 90.00
b = 72.179β = 90.00
c = 79.238γ = 90.00
Software Package:
Software NamePurpose
PROCESSdata reduction
PROCESSdata scaling
REFMACrefinement
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-08-03 
  • Released Date: 2010-08-04 
  • Deposition Author(s): Suzuki, M.

Revision History 

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance