4A7I | pdb_00004a7i

Factor Xa in complex with a potent 2-amino-ethane sulfonamide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4A7I/pdb

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


• Deposited: 2011-11-14 Released: 2012-02-01 
• Deposition Author(s): Nazare, M., Matter, H., Will, D.W., Wagner, M., Urmann, M., Czech, J., Schreuder, H., Bauer, A., Ritter, K., Wehner, V.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: other

Literature

Fragment Deconstruction of Small, Potent Factor Xa Inhibitors: Exploring the Superadditivity Energetics of Fragment Linking in Protein-Ligand Complexes.

Nazare, M., Matter, H., Will, D.W., Wagner, M., Urmann, M., Czech, J., Schreuder, H., Bauer, A., Ritter, K., Wehner, V.

(2012) Angew Chem Int Ed Engl 51: 905

• PubMed: 22190348 
• DOI: https://doi.org/10.1002/anie.201107091
• Primary Citation Related Structures: 
  4A7I

---

Organizational Affiliation: 
• Sanofi-Aventis Deutschland GmbH, R&D, Industriepark Höchst, Building G878, 65926 Frankfurt am Main, Germany. [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: 39.52 kDa 
• Atom Count: 2,478 
• Modeled Residue Count: 287 
• Deposited Residue Count: 350 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FACTOR X LIGHT CHAIN	A	96	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
ACTIVATED FACTOR XA HEAVY CHAIN XA	B	254	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
A7I	D [auth B]	5-CHLORO-THIOPHENE-2-CARBOXYLIC ACID [2-(1--ISOPROPYL-PIPERIDIN-4-YLSULFAMOYL)-ETHYL]-AMIDE C15 H24 Cl N3 O3 S2 XIOBNAKYNXSFFO-UHFFFAOYSA-N
CA	C [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
A7I	BindingDB:  4A7I	Ki: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.253	α = 90
b = 72.042	β = 90
c = 77.416	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-01 
Deposition Author(s): Nazare, M., Matter, H., Will, D.W., Wagner, M., Urmann, M., Czech, J., Schreuder, H., Bauer, A., Ritter, K., Wehner, V.

Revision History  

• Version 1.0: 2012-02-01
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary