Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34711.00 
• Atom Count: 2362 
• Residue Count: 296 
• Unique protein chains: 3

2R2M

2-(2-Chloro-6-Fluorophenyl)Acetamides as Potent Thrombin Inhibitors

• DOI: 10.2210/pdb2R2M/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, Hirudo medicinalis


• Deposited: 2007-08-27 Released: 2008-08-26 
• Deposition Author(s): Spurlino, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.214 
• R-Value Work: 0.168 

Literature

2-(2-Chloro-6-Fluorophenyl)Acetamides as Potent Thrombin Inhibitors

Lee, L., Kreutter, K.D., Pan, W., Crysler, C., Spurlino, J., Player, M.R., Tomczuk, B., Lu, T.

(2007) Bioorg.Med.Chem.Lett. 17: 6266-6269

• PubMed: 17889527 
• DOI: 10.1016/j.bmcl.2007.09.013


• PubMed Abstract: 
  

2-(2-Chloro-6-fluorophenyl)acetamides having 2,2-difluoro-2-aryl/heteroaryl-ethylamine P3 and oxyguanidine P1 substituents are potent thrombin inhibitors (K(i)=0.9-33.9 nM). 2-(5-Chloro-pyridin-2-yl)-2,2-difluoroethylamine was the best P3 substituent, yielding the most potent inhibitor (K(i)=0.7 nM). Replacing the P3 heteroaryl group with a phenyl ring or replacing the difluoro substitution with dimethyl or cyclopropyl groups in the linker reduced the affinity for thrombin significantly. The aminopyridine P1s also provided an increase in potency.

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Organizational Affiliation: 

Drug Discovery, Johnson & Johnson, Pharmaceutical Research and Development, Spring House, PA, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Thrombin light chain	A	26	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Thrombin heavy chain	B	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Hirudin-3A	H	11	Hirudo medicinalis	Mutation(s): 0
Find proteins for P09945 (Hirudo medicinalis) Go to UniProtKB:  P09945

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
I50	B	N-[2-({[amino(imino)methyl]amino}oxy)ethyl]-2-{6-chloro-3-[(2,2-difluoro-2-phenylethyl)amino]-2-fluorophenyl}acetamide C19 H21 Cl F3 N5 O2 DZEJHPMTDNDECN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
I50	Ki: 47.1 nM BINDINGMOAD
I50	Ki: 47.1 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.214 
• R-Value Work: 0.168 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 70.950	α = 90.00
b = 72.135	β = 100.64
c = 72.850	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
X-PLOR	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-08-27 
• Released Date: 2008-08-26 
• Deposition Author(s): Spurlino, J.

Revision History 

• Version 1.0: 2008-08-26
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance