1ZGV | pdb_00001zgv

Thrombin in complex with an oxazolopyridine inhibitor 2

• PDB DOI: https://doi.org/10.2210/pdb1ZGV/pdb

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


• Deposited: 2005-04-22 Released: 2005-09-27 
• Deposition Author(s): Deng, J.Z., McMasters, D.R., Rabbat, P.M., Williams, P.D., Coburn, C.A., Yan, Y., Kuo, L.C., Lewis, S.D., Lucas, B.J., Krueger, J.A., Strulovici, B., Vacca, J.P., Lyle, T.A., Burgey, C.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.228 (Depositor) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Development of an oxazolopyridine series of dual thrombin/factor Xa inhibitors via structure-guided lead optimization.

Deng, J.Z., McMasters, D.R., Rabbat, P.M., Williams, P.D., Coburn, C.A., Yan, Y., Kuo, L.C., Lewis, S.D., Lucas, B.J., Krueger, J.A., Strulovici, B., Vacca, J.P., Lyle, T.A., Burgey, C.S.

(2005) Bioorg Med Chem Lett 15: 4411-4416

• PubMed: 16137886 
• DOI: https://doi.org/10.1016/j.bmcl.2005.07.022
• Primary Citation Related Structures: 
  1ZGI, 1ZGV


• PubMed Abstract: 
  

  Thrombin-inhibitor X-ray crystal structures, in combination with the installation of binding elements optimized within the pyrazinone series of thrombin inhibitors, were utilized to transform a weak triazolopyrimidine lead into a series of potent oxazolopyridines. A modification intended to attenuate plasma protein binding (i.e., conversion of the P3 pyridine to a piperidine) conferred significant factor Xa activity to this series. Ultimately, these dual thrombin/factor Xa inhibitors demonstrated excellent in vitro and in vivo anticoagulant efficacy.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.

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: 34.79 kDa 
• Atom Count: 2,417 
• Modeled Residue Count: 286 
• Deposited Residue Count: 297 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin	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
Hirudin	B	10	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P01050 (Hirudo medicinalis) Explore P01050  Go to UniProtKB:  P01050

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
501	C [auth A]	N7-BUTYL-N2-(5-CHLORO-2-METHYLPHENYL)-5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDINE-2,7-DIAMINE C17 H21 Cl N6 ZTYBIJUAAWLJNU-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
501	BindingDB:  1ZGV	IC50: 1000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.228 (Depositor) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.34	α = 90
b = 72.33	β = 101.07
c = 73.02	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-27 
Deposition Author(s): Deng, J.Z., McMasters, D.R., Rabbat, P.M., Williams, P.D., Coburn, C.A., Yan, Y., Kuo, L.C., Lewis, S.D., Lucas, B.J., Krueger, J.A., Strulovici, B., Vacca, J.P., Lyle, T.A., Burgey, C.S.

Revision History  

• Version 1.0: 2005-09-27
  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: 2012-12-12
  Changes: Other
• Version 1.4: 2013-03-13
  Changes: Other
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary