2J4I | pdb_00002j4i

CRYSTAL STRUCTURE OF A HUMAN FACTOR XA INHIBITOR COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb2J4I/pdb

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


• Deposited: 2006-08-31 Released: 2006-09-27 
• Deposition Author(s): Young, R.J., Campbell, M., Borthwick, A.D., Brown, D., Chan, C., Convery, M.A., Crowe, M.C., Dayal, S., Diallo, H., Kelly, H.A., Paul King, N., Kleanthous, S., Kurtis, C.L., Mason, A.M., Mordaunt, J.E., Patel, C., Pateman, A.J., Senger, S., Shah, G.P., Smith, P.W., Watson, N.S., Weston, H.E., Zhou, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.234 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Structure- and Property-Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Acyclic Alanyl Amides as P4 Motifs.

Young, R.J., Campbell, M., Borthwick, A.D., Brown, D., Burns-Kurtis, C.L., Chan, C., Convery, M.A., Crowe, M.C., Dayal, S., Diallo, H., Kelly, H.A., Paul King, N., Kleanthous, S., Mason, A.M., Mordaunt, J.E., Patel, C., Pateman, A.J., Senger, S., Shah, G.P., Smith, P.W., Watson, N.S., Weston, H.E., Zhou, P.

(2006) Bioorg Med Chem Lett 16: 5953

• PubMed: 16982190 
• DOI: https://doi.org/10.1016/j.bmcl.2006.09.001
• Primary Citation of Related Structures:  
  2J4I


• PubMed Abstract: 
  

  Structure-based drug design was exploited in the synthesis of 3-(6-chloronaphth-2-ylsulfonyl)aminopyrrolidin-2-one-based factor Xa (fXa) inhibitors, incorporating an alanylamide P4 group with acyclic tertiary amide termini. Optimized hydrophobic contacts of one amide substituent in P4 were complemented by hydrophobicity-modulating features in the second, producing potent fXa inhibitors including examples with excellent anticoagulant properties.

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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: 44.36 kDa 
• Atom Count: 2,457 
• Modelled Residue Count: 284 
• Deposited Residue Count: 388 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR X	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	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSJ	C [auth A]	1-PYRROLIDINEACETAMIDE, 3-[[(6-CHLORO-2-NAPHTHALENYL)SULFONYL]AMINO]-ALPHA-METHYL-N-(1-METHYLETHYL)-N-[2-[(METHYLSULFONYL)AMINO]ETHYL]-2-OXO-, (ALPHAS,3S)- C23 H31 Cl N4 O6 S2 MTIPCPPIOZUMIV-KKSFZXQISA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GSJ	BindingDB:  2J4I	Ki: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.234 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.192 (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): Young, R.J., Campbell, M., Borthwick, A.D., Brown, D., Chan, C., Convery, M.A., Crowe, M.C., Dayal, S., Diallo, H., Kelly, H.A., Paul King, N., Kleanthous, S., Kurtis, C.L., Mason, A.M., Mordaunt, J.E., Patel, C., Pateman, A.J., Senger, S., Shah, G.P., Smith, P.W., Watson, N.S., Weston, H.E., Zhou, P.

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, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary