2C8W

thrombin inhibitors

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Application of Fragment Screening and Fragment Linking to the Discovery of Novel Thrombin Inhibitors

Howard, N., Abell, C., Blakemore, W., Chessari, G., Congreve, M., Howard, S., Jhoti, H., Murray, C.W., Seavers, L.C.A., Van Montfort, R.L.M.

(2006) J Med Chem 49: 1346

  • DOI: 10.1021/jm050850v
  • Primary Citation of Related Structures:  
    2C8W, 2C8X, 2C8Y, 2C8Z, 2C90, 2C93

  • PubMed Abstract: 

    • The screening of fragments is an alternative approach to high-throughput screening for the identification of leads for therapeutic targets. Fragment hits have been discovered using X-ray crystallographic screening of protein crystals of the serine protease enzyme thrombin ...

    The screening of fragments is an alternative approach to high-throughput screening for the identification of leads for therapeutic targets. Fragment hits have been discovered using X-ray crystallographic screening of protein crystals of the serine protease enzyme thrombin. The fragment library was designed to avoid any well-precedented, strongly basic functionality. Screening hits included a novel ligand (3), which binds exclusively to the S2-S4 pocket, in addition to smaller fragments which bind to the S1 pocket. The structure of these protein-ligand complexes are presented. A chemistry strategy to link two such fragments together and to synthesize larger drug-sized compounds resulted in the efficient identification of hybrid inhibitors with nanomolar potency (e.g., 7, IC50 = 3.7 nM). These potent ligands occupy the same area of the active site as previously described peptidic inhibitors, while having very different chemical architecture.

    Organizational Affiliation: 

    Astex Therapeutics, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THROMBIN LIGHT CHAINA36Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
THROMBIN HEAVY CHAINB259Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HIRUDIN VARIANT-2C [auth I]12Hirudo medicinalisMutation(s): 0 
UniProt
Find proteins for P09945 (Hirudo medicinalis)
Explore P09945 
Go to UniProtKB:  P09945
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09945
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C7M
Query on C7M
Download Ideal Coordinates CCD File 
E [auth B](2S,3R)-N-[5-CHLORO-2-(2,3-DIHYDRO-1H-TETRAZOL-1-YL)BENZYL]-3-HYDROXY-4-{[(4-METHOXYPHENYL)SULFONYL]AMINO}-1-PHENYLBUTA N-2-AMINIUM
C25 H30 Cl N6 O4 S
LMFQPEFBZUDVPR-UKILVPOCSA-O		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
D [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS		C [auth I]L-PEPTIDE LINKINGC9 H11 N O6 STYR
Binding Affinity Annotations 
IDSourceBinding Affinity
C7M PDBBind:  2C8W IC50: 3.7 (nM) from 1 assay(s)
Binding MOAD:  2C8W IC50: 3.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.579α = 90
b = 71.906β = 100.42
c = 72.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
IN-HOUSEphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-04
    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: 2013-08-07
    Changes: Derived calculations, Other
  • Version 1.3: 2017-06-28
    Changes: Data collection