3C27 | pdb_00003c27

Cyanofluorophenylacetamides as Orally Efficacious Thrombin Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3C27/pdb

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


• Deposited: 2008-01-24 Released: 2009-02-17 
• Deposition Author(s): Spurlino, J.C., McMillan, M., Lewandowski, F., Milligan, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.215 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Cyanofluorophenylacetamides as Orally Efficacious Thrombin Inhibitors

Kreuter, K.D., Lee, L., Lu, T., Giardino, E.C., Patel, S., Haung, H., Xu, G., Fitzgerald, M., Mohan, M., Crysler, C., Eisennagel, S., Dasgupta, M., McMillan, M., Spurlino, J.C., Heubert, N., Maryanoff, B.E., Tomczuk, B.E., Damiano, B.P., Player, M.R.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 34.7 kDa 
• Atom Count: 2,473 
• Modeled Residue Count: 286 
• Deposited Residue Count: 296 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	A	26	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
Thrombin heavy chain	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 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin-3A	C [auth H]	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
DKK	D [auth B]	N-[2-(carbamimidamidooxy)ethyl]-2-{6-cyano-3-[(2,2-difluoro-2-pyridin-2-ylethyl)amino]-2-fluorophenyl}acetamide C19 H20 F3 N7 O2 STHCHQXQLDMISY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DKK	BindingDB:  3C27	Ki: 1.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.215 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.854	α = 90
b = 72.026	β = 100.5
c = 72.987	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-17 
Deposition Author(s): Spurlino, J.C., McMillan, M., Lewandowski, F., Milligan, C.

Revision History  

• Version 1.0: 2009-02-17
  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: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary