3IIT

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

• PDB DOI: https://doi.org/10.2210/pdb3IIT/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


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

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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 

Starting Model: experimental

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

• PubMed: 19900814 
• DOI: https://doi.org/10.1016/j.bmc.2009.10.024
• Primary Citation of Related Structures:  
  3IIT


• 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 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.

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Organizational Affiliation: 

R&D Division, Daiichi Sankyo Co, Ltd, 1-16-13, Kita-Kasai, Tokyo 134-8630, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.81 kDa 
• Atom Count: 2,398 
• Modelled Residue Count: 287 
• Deposited Residue Count: 287 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Activated factor Xa heavy chain	A	233	Homo sapiens	Mutation(s): 0  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742 GTEx:  ENSG00000126218

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Factor X light chain	B	54	Homo sapiens	Mutation(s): 0  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742 GTEx:  ENSG00000126218

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D14	E [auth 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
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
D14	PDBBind:  3IIT	IC50: 9.5 (nM) from 1 assay(s)
	BindingDB:  3IIT	IC50: 9.5 (nM) from 1 assay(s)

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 = 56.055	α = 90
b = 72.179	β = 90
c = 79.238	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROCESS	data reduction
PROCESS	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary