Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 34.94 kDa 
• Atom Count: 2,504 
• Modelled Residue Count: 287 
• Deposited Residue Count: 298 
• Unique protein chains: 2

 1TA6

Crystal structure of thrombin in complex with compound 14b

• PDB DOI: 10.2210/pdb1TA6/pdb

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


• Deposited: 2004-05-19 Released: 2004-06-08 
• Deposition Author(s): Tucker, T.J., Brady, S.F., Lumma, W.C., Lewis, S.D., Gardel, S.J., Naylor-Olsen, A.M., Yan, Y., Sisko, J.T., Stauffer, K.J., Lucas, B.Y., Lynch, J.J., Cook, J.J., Stranieri, M.T., Holahan, M.A., Lyle, E.A., Baskin, E.P., Chen, I.-W., Dancheck, K.B., Krueger, J.A., Cooper, C.M., Vacca, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Work: 0.186 
• R-Value Observed: 0.186 

Literature

Design and synthesis of a series of potent and orally bioavailable noncovalent thrombin inhibitors that utilize nonbasic groups in the P1 position

Tucker, T.J., Brady, S.F., Lumma, W.C., Lewis, S.D., Gardel, S.J., Naylor-Olsen, A.M., Yan, Y., Sisko, J.T., Stauffer, K.J., Lucas, B.Y., Lynch, J.J., Cook, J.J., Stranieri, M.T., Holahan, M.A., Lyle, E.A., Baskin, E.P., Chen, I.-W., Dancheck, K.B., Krueger, J.A., Cooper, C.M., Vacca, J.P.

(1998) J Med Chem 41: 3210-3219

• PubMed: 9703466 
• DOI: 10.1021/jm9801713
• Primary Citation of Related Structures:  
  1TA2, 1TA6


• PubMed Abstract: 
  

As part of an ongoing effort to prepare therapeutically useful orally active thrombin inhibitors, we have synthesized a series of compounds that utilize nonbasic groups in the P1 position. The work is based on our previously reported lead structure, compound 1, which was discovered via a resin-based approach to varying P1. By minimizing the size and lipophilicity of the P3 group and by incorporating hydrogen-bonding groups on the N-terminus or on the 2-position of the P1 aromatic ring, we have prepared a number of derivatives in this series that exhibit subnanomolar enzyme potency combined with good in vivo antithrombotic and bioavailability profiles. The oxyacetic amide compound 14b exhibited the best overall profile of in vitro and in vivo activity, and crystallographic studies indicate a unique mode of binding in the thrombin active site.

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Organizational Affiliation: 

Departments of Medicinal Chemistry, Biological Chemistry, Pharmacology, Drug Metabolism, and Molecular Design and Diversity, Merck Research Laboratories, West Point, Pennsylvania 19486, USA.

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
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
Hirudin	B	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
177	C [auth A]	1-[2-AMINO-2-CYCLOHEXYL-ACETYL]-PYRROLIDINE-3-CARBOXYLIC ACID 5-CHLORO-2-(2-ETHYLCARBAMOYL-ETHOXY)-BENZYLAMIDE C24 H35 Cl N4 O4 BMHVHOJXEQTIEA-SIKLNZKXSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
177	BindingDB:  1TA6	Ki: 0.74 (nM) from 1 assay(s)
	PDBBind:  1TA6	Ki: 0.74 (nM) from 1 assay(s)
	Binding MOAD:  1TA6	Ki: 0.74 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Work: 0.186 
• R-Value Observed: 0.186 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.4	α = 90
b = 72.14	β = 101
c = 73.52	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-08 
Deposition Author(s): Tucker, T.J., Brady, S.F., Lumma, W.C., Lewis, S.D., Gardel, S.J., Naylor-Olsen, A.M., Yan, Y., Sisko, J.T., Stauffer, K.J., Lucas, B.Y., Lynch, J.J., Cook, J.J., Stranieri, M.T., Holahan, M.A., Lyle, E.A., Baskin, E.P., Chen, I.-W., Dancheck, K.B., Krueger, J.A., Cooper, C.M., Vacca, J.P.

Revision History  

• Version 1.0: 2004-06-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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