1SL3 | pdb_00001sl3

crystal structue of Thrombin in complex with a potent P1 heterocycle-Aryl based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 
    0.240 (Depositor) 
  • R-Value Work: 
    0.210 (Depositor) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1SL3

This is version 1.4 of the entry. See complete history

Literature

Discovery and evaluation of potent P1 aryl heterocycle-based thrombin inhibitors

Young, M.B.Barrow, J.C.Glass, K.L.Lundell, G.F.Newton, C.L.Pellicore, J.M.Rittle, K.E.Selnick, H.G.Stauffer, K.J.Vacca, J.P.Williams, P.D.Bohn, D.Clayton, F.C.Cook, J.J.Krueger, J.A.Kuo, L.C.Lewis, S.D.Lucas, B.J.McMasters, D.R.Miller-Stein, C.Pietrak, B.L.

(2004) J Med Chem 47: 2995-3008

  • DOI: https://doi.org/10.1021/jm030303e
  • Primary Citation Related Structures: 
    1SL3

  • PubMed Abstract: 

    In an effort to discover potent, clinically useful thrombin inhibitors, a rapid analogue synthetic approach was used to explore the P(1) region. Various benzylamines were coupled to a pyridine/pyrazinone P(2)-P(3) template. One compound with an o-thiadiazole benzylic substitution was found to have a thrombin K(i) of 0.84 nM. A study of ortho-substituted five-membered-ring heterocycles was undertaken and subsequently demonstrated that the o-triazole and tetrazole rings were optimal. Combination of these potent P(1) aryl heterocycles with a variety of P(2)-P(3) groups produced a compound with an extraordinary thrombin inhibitory activity of 1.4 pM. It is hoped that this potency enhancement in P(1) will allow for more diversification in the P(2)-P(3) region to ultimately address additional pharmacological concerns.


  • Organizational Affiliation
    • Medicinal Chemistry, Merck Research Laboratories, Merck and Co., Inc., WP14-3, Post Office Box 4, Sumneytown Pike, West Point, PA 19486, USA. mary_beth_young@merck.com

Macromolecule Content 

  • Total Structure Weight: 35.07 kDa 
  • Atom Count: 2,655 
  • Modeled Residue Count: 287 
  • Deposited Residue Count: 298 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
thrombin287Homo sapiensMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hirudin11Hirudo medicinalisMutation(s): 0 
UniProt
Find proteins for P28504 (Hirudo medicinalis)
Explore P28504 
Go to UniProtKB:  P28504
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28504
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
170

Query on 170



Download:Ideal Coordinates CCD File
C [auth A](2-[6-CHLORO-3-{[2,2-DIFLUORO-2-(1-OXIDOPYRIDIN-2-YL)ETHYL]AMINO}-2-OXOPYRAZIN-1(2H)-YL]-N-[5-CHLORO-2-(1H-TETRAZOL-1-YL)BENZYL]ACETAMIDE
C21 H17 Cl2 F2 N9 O3
QOKFRQVFMZFNBC-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
B
L-PEPTIDE LINKINGC9 H11 N O6 STYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free:  0.240 (Depositor) 
  • R-Value Work:  0.210 (Depositor) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70α = 90
b = 71.5β = 100.6
c = 72.5γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-03
    Type: Initial release
  • Version 1.1: 2008-04-29
    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
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary