Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.01 kDa 
• Atom Count: 2,564 
• Modelled Residue Count: 287 
• Deposited Residue Count: 298 
• Unique protein chains: 2

 1Z71

thrombin and P2 pyridine N-oxide inhibitor complex structure

• PDB DOI:  https://doi.org/10.2210/pdb1Z71/pdb

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


• Deposited: 2005-03-23 Released: 2005-05-17 
• Deposition Author(s): Nantermet, P.G., Burgey, C.S., Robinson, K.A., Pellicore, J.M., Newton, C.L., Deng, J.Z., Lyle, T.A., Selnick, H.G., Lewis, S.D., Lucas, B.J., Krueger, J.A., Miller-Stein, C., White, R.B., Wong, B., McMasters, D.R., Wallace, A.A., Lynch Jr., J.J., Yan, Y., Chen, Z., Kuo, L., Gardell, S.J., Shafer, J.A., Vacca, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.254 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Literature

P(2) pyridine N-oxide thrombin inhibitors: a novel peptidomimetic scaffold

Nantermet, P.G., Burgey, C.S., Robinson, K.A., Pellicore, J.M., Newton, C.L., Deng, J.Z., Selnick, H.G., Lewis, S.D., Lucas, B.J., Krueger, J.A., Miller-Stein, C., White, R.B., Wong, B., McMasters, D.R., Wallace, A.A., Lynch Jr., J.J., Yan, Y., Chen, Z., Kuo, L., Gardell, S.J., Shafer, J.A., Vacca, J.P., Lyle, T.A.

(2005) Bioorg Med Chem Lett 15: 2771-2775

• PubMed: 15911253 
• DOI: https://doi.org/10.1016/j.bmcl.2005.03.110
• Primary Citation of Related Structures:  
  1Z71


• PubMed Abstract: 
  

In this study, we have demonstrated that the critical hydrogen bonding motif of the established 3-aminopyrazinone thrombin inhibitors can be effectively mimicked by a 2-aminopyridine N-oxide. As this peptidomimetic core is more resistant toward oxidative metabolism, it also overcomes the metabolic liability associated with the pyrazinones. An optimization study of the P(1) benzylamide delivered the potent thrombin inhibitor 21 (K(i) = 3.2 nM, 2xaPTT = 360 nM), which exhibited good plasma levels and half-life after oral dosing in the dog (C(max) = 2.6 microM, t(1/2) = 4.5 h).

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Organizational Affiliation: 

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

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 IIIB'	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
L17	C [auth A]	L17 C22 H20 Cl2 F2 N4 O3 ISTCYDGUBPNUDF-CQSZACIVSA-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
L17	Binding MOAD:  1Z71	Ki: 0.66 (nM) from 1 assay(s)
	PDBBind:  1Z71	Ki: 0.66 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.254 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.97	α = 90
b = 71.49	β = 100.5
c = 72.26	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-17 
Deposition Author(s): Nantermet, P.G., Burgey, C.S., Robinson, K.A., Pellicore, J.M., Newton, C.L., Deng, J.Z., Lyle, T.A., Selnick, H.G., Lewis, S.D., Lucas, B.J., Krueger, J.A., Miller-Stein, C., White, R.B., Wong, B., McMasters, D.R., Wallace, A.A., Lynch Jr., J.J., Yan, Y., Chen, Z., Kuo, L., Gardell, S.J., Shafer, J.A., Vacca, J.P.

Revision History  

• Version 1.0: 2005-05-17
  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: 2017-10-11
  Changes: Refinement description