Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.8 kDa 
• Atom Count: 2,470 
• Modelled Residue Count: 287 
• Deposited Residue Count: 306 
• Unique protein chains: 3

 1MU6

Crystal Structure of Thrombin in Complex with L-378,622

• PDB DOI:  https://doi.org/10.2210/pdb1MU6/pdb

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


• Deposited: 2002-09-23 Released: 2004-04-06 
• Deposition Author(s): Burgey, C.S., Robinson, K.A., Lyle, T.A., Sanderson, P.E., Lewis, S.D., Lucas, B.J., Krueger, J.A., Singh, R., Miller-Stein, C., White, R.B., Wong, B., Lyle, E.A., Williams, P.D., Coburn, C.A., Dorsey, B.D., Barrow, J.C., Stranieri, M.T., Holahan, M.A., Sitko, G.R., Cook, J.J., McMasters, D.R., McDonough, C.M., Sanders, W.M., Wallace, A.A., Clayton, F.C., Bohn, D., Leonard, Y.M., Detwiler Jr., T.J., Lynch Jr., J.J., Yan, Y., Chen, Z., Kuo, L., Gardell, S.J., Shafer, J.A., Vacca, J.P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.235 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

Literature

Metabolism-directed optimization of 3-aminopyrazinone acetamide thrombin inhibitors. Development of an orally bioavailable series containing P1 and P3 pyridines.

Burgey, C.S., Robinson, K.A., Lyle, T.A., Sanderson, P.E., Lewis, S.D., Lucas, B.J., Krueger, J.A., Singh, R., Miller-Stein, C., White, R.B., Wong, B., Lyle, E.A., Williams, P.D., Coburn, C.A., Dorsey, B.D., Barrow, J.C., Stranieri, M.T., Holahan, M.A., Sitko, G.R., Cook, J.J., McMasters, D.R., McDonough, C.M., Sanders, W.M., Wallace, A.A., Clayton, F.C., Bohn, D., Leonard, Y.M., Detwiler Jr., T.J., Lynch Jr., J.J., Yan, Y., Chen, Z., Kuo, L., Gardell, S.J., Shafer, J.A., Vacca, J.P.J.

(2003) J Med Chem 46: 461-473

• PubMed: 12570369 
• DOI: https://doi.org/10.1021/jm020311f
• Primary Citation of Related Structures:  
  1MU6, 1MU8


• PubMed Abstract: 
  

Recent efforts in the field of thrombin inhibitor research have focused on the identification of compounds with good oral bioavailability and pharmacokinetics. In this manuscript we describe a metabolism-based approach to the optimization of the 3-(2-phenethylamino)-6-methylpyrazinone acetamide template (e.g., 1) which resulted in the modification of each of the three principal components (i.e., P1, P2, P3) comprising this series. As a result of these studies, several potent thrombin inhibitors (e.g., 20, 24, 25) were identified which exhibit high levels of oral bioavailability and long plasma half-lives.

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Organizational Affiliation: 

Departments of Medicinal Chemistry, Biological Chemistry, Drug Metabolism, Molecular Systems, Structural Biology, and Pharmacology, Merck Research Laboratories, West Point, Pennsylvania 19486, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN	A	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN	B	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIRUDIN IIB	C	11	Hirudo medicinalis	Mutation(s): 0
UniProt
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
CDA	D [auth B]	2-(6-CHLORO-3-{[2,2-DIFLUORO-2-(2-PYRIDINYL)ETHYL]AMINO}-2-OXO-1(2H)-PYRAZINYL)-N-[(2-FLUORO-6-PYRIDINYL)METHYL]ACETAMIDE C20 H19 F3 N6 O2 JXHWVKOKYDAROD-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
CDA	Binding MOAD:  1MU6	Ki: 4.2 (nM) from 1 assay(s)
	PDBBind:  1MU6	Ki: 4.2 (nM) from 1 assay(s)
	BindingDB:  1MU6	Ki: 4.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.235 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.22	α = 90
b = 72.21	β = 101.1
c = 73.3	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-06 
Deposition Author(s): Burgey, C.S., Robinson, K.A., Lyle, T.A., Sanderson, P.E., Lewis, S.D., Lucas, B.J., Krueger, J.A., Singh, R., Miller-Stein, C., White, R.B., Wong, B., Lyle, E.A., Williams, P.D., Coburn, C.A., Dorsey, B.D., Barrow, J.C., Stranieri, M.T., Holahan, M.A., Sitko, G.R., Cook, J.J., McMasters, D.R., McDonough, C.M., Sanders, W.M., Wallace, A.A., Clayton, F.C., Bohn, D., Leonard, Y.M., Detwiler Jr., T.J., Lynch Jr., J.J., Yan, Y., Chen, Z., Kuo, L., Gardell, S.J., Shafer, J.A., Vacca, J.P.J.

Revision History  

• Version 1.0: 2004-04-06
  Type: Initial release
  
• Version 1.1: 2008-04-28
  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: 2012-12-12
  Changes: Other
• Version 1.4: 2013-03-13
  Changes: Other
• Version 1.5: 2021-07-21
  Changes: Derived calculations, Refinement description