2PKS

Thrombin in complex with inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Design, synthesis and biological evaluation of thrombin inhibitors based on a pyridine scaffold.

Blomberg, D., Fex, T., Xue, Y., Brickmann, K., Kihlberg, J.

(2007) Org Biomol Chem 5: 2599-2605

  • DOI: 10.1039/b705344d
  • Primary Citation of Related Structures:  
    2PKS

  • PubMed Abstract: 

    • A series of 2,4-disubstituted pyridine derivatives has been designed, synthesised and evaluated as thrombin inhibitors. A Grignard exchange reaction was used to introduce various benzoyl substituents in position 4 of the pyridine ring, where they serve as P3 residues in binding to thrombin ...

    A series of 2,4-disubstituted pyridine derivatives has been designed, synthesised and evaluated as thrombin inhibitors. A Grignard exchange reaction was used to introduce various benzoyl substituents in position 4 of the pyridine ring, where they serve as P3 residues in binding to thrombin. In position 2 of the pyridine ring, a para-amidinobenzylamine moiety was incorporated as P1 residue by an SNAr reaction using ammonia as nucleophile followed by a reductive amination. A crystal structure obtained for one of the compounds in the active site of thrombin revealed that the basic amidine group of the inhibitor was anchored to Asp 189 at the bottom of the S1 pocket. A comparison with melagatran, bound in the active site of thrombin, revealed a good shape match but lack of hydrogen bonding possibilities in the S2-S3 region for the thrombin inhibitors reported in this study.

    Organizational Affiliation: 

    Organic Chemistry, Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin light chain A27Homo 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
GTEx:  ENSG00000180210
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin heavy chain fragment B147Homo 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
GTEx:  ENSG00000180210
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin heavy chain fragment C102Homo 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
GTEx:  ENSG00000180210
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Hirudin D10N/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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G44
Query on G44
Download Ideal Coordinates CCD File 
C
4-({[4-(3-METHYLBENZOYL)PYRIDIN-2-YL]AMINO}METHYL)BENZENECARBOXIMIDAMIDE
C21 H20 N4 O
MBJYEMUMDMGQQC-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS		DL-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G44IC50 :  11000   nM  PDBBind
G44IC50:  11000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.942α = 90
b = 71.843β = 100.23
c = 70.778γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2007-04-18 
  • Released Date: 2008-04-22 
    • Deposition Author(s): Xue, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description