3C1K

Crystal structure of thrombin in complex with inhibitor 15

• PDB DOI: https://doi.org/10.2210/pdb3C1K/pdb

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


• Deposited: 2008-01-23 Released: 2008-03-18 
• Deposition Author(s): Yan, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

Structure-based design of novel groups for use in the P1 position of thrombin inhibitor scaffolds. Part 2: N-acetamidoimidazoles.

Isaacs, R.C., Solinsky, M.G., Cutrona, K.J., Newton, C.L., Naylor-Olsen, A.M., McMasters, D.R., Krueger, J.A., Lewis, S.D., Lucas, B.J., Kuo, L.C., Yan, Y., Lynch, J.J., Lyle, E.A.

(2008) Bioorg Med Chem Lett 18: 2062-2066

• PubMed: 18291642 
• DOI: https://doi.org/10.1016/j.bmcl.2008.01.098
• Primary Citation of Related Structures:  
  3C1K


• PubMed Abstract: 
  

  Guided by X-ray crystallography of thrombin-inhibitor complexes and molecular modeling, alkylation of the N1 nitrogen of the imidazole P1 ligand of the pyridinoneacetamide thrombin inhibitor 1 with various acetamide moieties furnished inhibitors with significantly improved thrombin potency, trypsin selectivity, functional in vitro anticoagulant potency and in vivo antithrombotic efficacy. In the pyrazinoneacetamide series, oral bioavailability was also improved.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA. [e-mail]

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: 35.11 kDa 
• Atom Count: 2,517 
• Modelled Residue Count: 287 
• Deposited Residue Count: 298 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A	287	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirugen	B	11	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P28511 (Hirudo medicinalis) Explore P28511  Go to UniProtKB:  P28511

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T15	C [auth A]	2-{3-[(benzylsulfonyl)amino]-6-methyl-2-oxopyridin-1(2H)-yl}-N-({1-[2-(tert-butylamino)-2-oxoethyl]-4-methyl-1H-imidazol-5-yl}methyl)acetamide C26 H34 N6 O5 S JIBFIIUWYBXSQB-UHFFFAOYSA-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
T15	PDBBind:  3C1K	Ki: 0.36 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.839	α = 90
b = 72.279	β = 101.19
c = 73.195	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Yan, Y.

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2012-12-12
  Changes: Other
• Version 1.3: 2013-03-13
  Changes: Other
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary