2J2U | pdb_00002j2u

CRYSTAL STRUCTURE OF A HUMAN FACTOR XA INHIBITOR COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb2J2U/pdb

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


• Deposited: 2006-08-17 Released: 2006-09-27 
• Deposition Author(s): Senger, S., Convery, M.A., Chan, C., Watson, N.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.236 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Arylsulfonamides: A Study of the Relationship between Activity and Conformational Preferences for a Series of Factor Xa Inhibitors.

Senger, S., Convery, M.A., Chan, C., Watson, N.S.

(2006) Bioorg Med Chem Lett 16: 5731

• PubMed: 16982192 
• DOI: https://doi.org/10.1016/j.bmcl.2006.08.092
• Primary Citation Related Structures: 
  2J2U, 2J34, 2J38


• PubMed Abstract: 
  

  Torsional scans of sulfonamide S-C bonds in small model systems of a series of arylsulfonamide factor Xa inhibitors were performed in order to investigate if conformational effects can help to rationalise the observed SAR. Computational results were in good agreement with the experimental data indicating that the sulfonamide conformation plays an important role in determining the activity in this particular series of factor Xa inhibitors.

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Organizational Affiliation: 
• GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 44.22 kDa 
• Atom Count: 2,418 
• Modeled Residue Count: 281 
• Deposited Residue Count: 388 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR X HEAVY CHAIN	A	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR X LIGHT CHAIN	B	134	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSQ	C [auth A]	5-CHLORO-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-5-CHLORO-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-SULFONAMIDE C19 H23 Cl N4 O5 S BHNMMFGOJRIAEZ-LRDDRELGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.236 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.862	α = 90
b = 72.862	β = 90
c = 78.142	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-27 
Deposition Author(s): Senger, S., Convery, M.A., Chan, C., Watson, N.S.

Revision History  

• Version 1.0: 2006-09-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary