1NM6

thrombin in complex with selective macrocyclic inhibitor at 1.8A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Design and synthesis of potent and selective macrocyclic thrombin inhibitors

Nantermet, P.G.Barrow, J.C.Newton, C.L.Pellicore, J.M.Young, M.Lewis, S.D.Lucas, B.J.Krueger, J.A.McMasters, D.R.Yan, Y.Kuo, L.C.Vacca, J.P.Selnick, H.G.

(2003) Bioorg Med Chem Lett 13: 2781-2784

  • DOI: 10.1016/s0960-894x(03)00506-7
  • Primary Citation of Related Structures:  
    1NM6, 1NT1

  • PubMed Abstract: 
  • A series of potent and selective proline- and pyrazinone-based macrocyclic thrombin inhibitors is described. Detailed SAR studies led to the incorporation of specific functional groups in the tether that enhanced functional activity against thrombin ...

    A series of potent and selective proline- and pyrazinone-based macrocyclic thrombin inhibitors is described. Detailed SAR studies led to the incorporation of specific functional groups in the tether that enhanced functional activity against thrombin and provided exquisite selectivity against trypsin and tPA. X-ray crystallography and molecular modeling studies revealed the inhibitor-enzyme interactions responsible for this selectivity.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA. philippe_nanternet@merck.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
thrombinA287Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HirudinB11N/AMutation(s): 0 
Find proteins for P28504 (Hirudo medicinalis)
Explore P28504 
Go to UniProtKB:  P28504
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L86
Query on L86

Download CCD File 
A
(11S)-11-BENZYL-6-CHLORO-1,2,10,11,12,13,14,15,16,17,18,19-DODECAHYDRO-5,9-METHANO-2,5,8,10,13,17-BENZOHEXAAZACYCLOHENI COSINE-3,24-DIONE
C27 H33 Cl N6 O2
LYVSCNRRXJZCRV-QHCPKHFHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
BL-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L86Ki:  0.09000000357627869   nM  Binding MOAD
L86Ki:  0.09000000357627869   nM  BindingDB
L86Ki :  0.09000000357627869   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.7α = 90
b = 71.4β = 100.5
c = 72.3γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-02
    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