Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.07 kDa 
• Atom Count: 2655 
• Residue Count: 287 
• Unique protein chains: 2

1SL3

crystal structue of Thrombin in complex with a potent P1 heterocycle-Aryl based inhibitor

• DOI: 10.2210/pdb1SL3/pdb

• Classification: BLOOD CLOTTING,HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens, Hirudo medicinalis
• Mutation(s): No 


• Deposited: 2004-03-05 Released: 2004-08-03 
• Deposition Author(s): Young, M.B., Barrow, J.C., Glass, K.L., Lundell, G.F., Newton, C.L., Pellicore, J.M., Rittle, K.E., Selnick, H.G., Stauffer, K.J., Vacca, J.P., Williams, P.D., Bohn, D., Clayton, F.C., Cook, J.J., Krueger, J.A., Kuo, L.C., Lewis, S.D., Lucas, B.J., McMasters, D.R., Miller-Stein, C., Pietrak, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.240 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 

Literature

Discovery and evaluation of potent P1 aryl heterocycle-based thrombin inhibitors

Young, M.B., Barrow, J.C., Glass, K.L., Lundell, G.F., Newton, C.L., Pellicore, J.M., Rittle, K.E., Selnick, H.G., Stauffer, K.J., Vacca, J.P., Williams, P.D., Bohn, D., Clayton, F.C., Cook, J.J., Krueger, J.A., Kuo, L.C., Lewis, S.D., Lucas, B.J., McMasters, D.R., Miller-Stein, C., Pietrak, B.L.

(2004) J Med Chem 47: 2995-3008

• PubMed: 15163182 
• DOI: 10.1021/jm030303e
• Primary Citation of Related Structures:  
  1SL3


• PubMed Abstract: 
  

In an effort to discover potent, clinically useful thrombin inhibitors, a rapid analogue synthetic approach was used to explore the P(1) region. Various benzylamines were coupled to a pyridine/pyrazinone P(2)-P(3) template. One compound with an o-thiadiazole benzylic substitution was found to have a thrombin K(i) of 0.84 nM. A study of ortho-substituted five-membered-ring heterocycles was undertaken and subsequently demonstrated that the o-triazole and tetrazole rings were optimal. Combination of these potent P(1) aryl heterocycles with a variety of P(2)-P(3) groups produced a compound with an extraordinary thrombin inhibitory activity of 1.4 pM. It is hoped that this potency enhancement in P(1) will allow for more diversification in the P(2)-P(3) region to ultimately address additional pharmacological concerns.

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Organizational Affiliation: 

Medicinal Chemistry, Merck Research Laboratories, Merck and Co., Inc., WP14-3, Post Office Box 4, Sumneytown Pike, West Point, PA 19486, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
thrombin	A	287	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin	B	11	Hirudo medicinalis	Mutation(s): 0
Find proteins for P28504 (Hirudo medicinalis) Explore P28504  Go to UniProtKB:  P28504

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
170	A	(2-[6-CHLORO-3-{[2,2-DIFLUORO-2-(1-OXIDOPYRIDIN-2-YL)ETHYL]AMINO}-2-OXOPYRAZIN-1(2H)-YL]-N-[5-CHLORO-2-(1H-TETRAZOL-1-YL)BENZYL]ACETAMIDE C21 H17 Cl2 F2 N9 O3 QOKFRQVFMZFNBC-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	B	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
170	Ki:  0.0014000000664964318   nM  Binding MOAD
170	Ki:  0   nM  BindingDB
170	Ki:  1.399999976158142   nM  BindingDB
170	Ki :  0.0014000000664964318   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.240 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70	α = 90
b = 71.5	β = 100.6
c = 72.5	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-03-05 
• Released Date: 2004-08-03 
Deposition Author(s): Young, M.B., Barrow, J.C., Glass, K.L., Lundell, G.F., Newton, C.L., Pellicore, J.M., Rittle, K.E., Selnick, H.G., Stauffer, K.J., Vacca, J.P., Williams, P.D., Bohn, D., Clayton, F.C., Cook, J.J., Krueger, J.A., Kuo, L.C., Lewis, S.D., Lucas, B.J., McMasters, D.R., Miller-Stein, C., Pietrak, B.L.

Revision History 

• Version 1.0: 2004-08-03
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description