3TU7

Human alpha-thrombin complexed with N-(methylsulfonyl)-D-phenylalanyl-N-((1-carbamimidoyl-4-piperidinyl)methyl)-l-prolinamide (BMS-189664)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular design and structure-activity relationships leading to the potent, selective, and orally active thrombin active site inhibitor BMS-189664.

Das, J.Kimball, S.D.Hall, S.E.Han, W.C.Iwanowicz, E.Lin, J.Moquin, R.V.Reid, J.A.Sack, J.S.Malley, M.F.Chang, C.Y.Chong, S.Wang-Iverson, D.B.Roberts, D.G.Seiler, S.M.Schumacher, W.A.Ogletree, M.L.

(2002) Bioorg.Med.Chem.Lett. 12: 45-49


  • PubMed Abstract: 
  • A series of structurally novel small molecule inhibitors of human alpha-thrombin was prepared to elucidate their structure-activity relationships (SARs), selectivity and activity in vivo. BMS-189664 (3) is identified as a potent, selective, and orall ...

    A series of structurally novel small molecule inhibitors of human alpha-thrombin was prepared to elucidate their structure-activity relationships (SARs), selectivity and activity in vivo. BMS-189664 (3) is identified as a potent, selective, and orally active reversible inhibitor of human alpha-thrombin which is efficacious in vivo in a mouse lethality model, and at inhibiting both arterial and venous thrombosis in cynomolgus monkey models.


    Organizational Affiliation

    Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543-4000, USA. jagabandhu.das@bms.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
L
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Prothrombin
H
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hirudin variant-2
I
12Hirudo medicinalisMutation(s): 0 
Find proteins for P09945 (Hirudo medicinalis)
Go to UniProtKB:  P09945
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0BM
Query on 0BM

Download SDF File 
Download CCD File 
H
N-(methylsulfonyl)-D-phenylalanyl-N-[(1-carbamimidoylpiperidin-4-yl)methyl]-L-prolinamide
C22 H34 N6 O4 S
UCVAQBJLJIKTFJ-MOPGFXCFSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000811 (0BM)
Query on PRD_000811
HN-(METHYLSULFONYL)-D-PHENYLALANYL-N-[(1-CARBAMIMIDOYLPIPERIDIN-4-YL)METHYL]-L-PROLINAMIDEPeptide-like / Thrombin inhibitor

--

Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
I
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0BMIC50: 46 nM BINDINGMOAD
0BMKi: 8.17 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.159 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 164.219α = 90.00
b = 48.952β = 90.00
c = 43.631γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
BUSTERrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-09-16 
  • Released Date: 2011-10-12 
  • Deposition Author(s): Malley, M., Sack, J.S.

Revision History 

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Other