3IIT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

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
  • Structures With Same Primary Citation

  • 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 chainA233Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Factor X light chainB54Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D14
Query on D14

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
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D14IC50:  9.5   nM  BindingDB
D14IC50 :  9.5   nM  PDBBind
D14IC50:  9.5   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.055α = 90
b = 72.179β = 90
c = 79.238γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PROCESSdata reduction
PROCESSdata scaling
REFMACphasing

Structure Validation

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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
    Changes: Version format compliance