2EI8

FACTOR XA IN COMPLEX WITH THE INHIBITOR (1S,2R,4S)-N1-[(5-chloroindol-2-yl)carbonyl]-4-(N,N-dimethylcarbamoyl)-N2-[(5-methyl-4,5,6,7-tetrahydrothiazolo[5,4-c]pyridin-2-yl)carbonyl]-1,2-cyclohexanediamine

• PDB DOI: https://doi.org/10.2210/pdb2EI8/pdb

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


• Deposited: 2007-03-12 Released: 2008-03-18 
• Deposition Author(s): Suzuki, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.250 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

Discovery of N-{(1R,2S,5S)-2-{[(5-Chloroindol-2-yl)carbonyl]amino}-5-[(dimethylamino)carbonyl]cyclohexyl}-5-methyl-4,5,6,7-tetrahydrothiazolo[5,4-c]pyridine-2-carboxamide hydrochloride: A Novel, Potent and Orally Active Direct Inhibitor of Factor Xa

Nagata, T., Yoshino, T., Haginoya, N., Yoshikawa, K., Nagamochi, M., Kobayashi, S., Komoriya, S., Yokomizo, A., Muto, R., Yamaguchi, K., Osanai, K., Suzuki, M., Kanno, H.

To be published.

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: 32.82 kDa 
• Atom Count: 2,373 
• Modelled Residue Count: 287 
• Deposited Residue Count: 287 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X, 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
Coagulation 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
DT8	E [auth A]	N-((1R,2S,5S)-2-(5-CHLORO-1H-INDOLE-2-CARBOXAMIDO)-5-(DIMETHYLCARBAMOYL)CYCLOHEXYL)-5-METHYL-4,5,6,7-TETRAHYDROTHIAZOLO[5,4-C]PYRIDINE-2-CARBOXAMIDE C26 H31 Cl N6 O3 S SZBHQQIIGORYND-ADLFWFRXSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DT8	BindingDB:  2EI8	Ki: min: 1.74, max: 8.77 (nM) from 3 assay(s)
		IC50: min: 2.3, max: 5.1 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.250 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.217	α = 90
b = 72.19	β = 90
c = 79.325	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Suzuki, M.

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary