2GDE

Thrombin in complex with inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Total synthesis and structural confirmation of chlorodysinosin A.

Hanessian, S., Del Valle, J.R., Xue, Y., Blomberg, N.

(2006) J Am Chem Soc 128: 10491-10495

  • DOI: 10.1021/ja0625834
  • Primary Citation of Related Structures:  
    2GDE

  • PubMed Abstract: 

    • The first enantiocontrolled total synthesis of the marine sponge metabolite chlorodysinosin A is described. The structure and absolute configuration are identical to those of dysinosin A except for the presence of a novel 2S,3R-3-chloroleucine residue in the former ...

    The first enantiocontrolled total synthesis of the marine sponge metabolite chlorodysinosin A is described. The structure and absolute configuration are identical to those of dysinosin A except for the presence of a novel 2S,3R-3-chloroleucine residue in the former. A concise stereocontrolled synthesis of the new chlorine-containing amino acid fragment was developed. An X-ray cocrystal structure of synthetic chlorodysinosin A with the enzyme thrombin confirms the structure and configuration assignment achieved through total synthesis. Within the aeruginosin family of natural products, chlorodysinosin A is the most potent inhibitor of the serine proteases thrombin, factor VIIa, and factor Xa, which are critical enzymes in the process leading to platelet aggregation and fibrin mesh formation in humans.

    Organizational Affiliation: 

    Department of Chemistry, Université de Montréal, C.P. 6128, Station Centre-ville, Montréal, P.Q., H3C 3J7 Canada.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin light chainA [auth L]36Homo 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 chainB [auth H]259Homo 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
HirudinC [auth D]10Hirudo medicinalisMutation(s): 0 
UniProt
Find proteins for P01050 (Hirudo medicinalis)
Explore P01050 
Go to UniProtKB:  P01050
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01050
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SN3
Query on SN3
Download Ideal Coordinates CCD File 
E [auth H](R)-3-((2S,3R)-1-((2S,3AR,5S,6S,7AS)-2-(2-(1-CARBAMIMIDOYL-2,5-DIHYDRO-1H-PYRROL-3-YL)ETHYLCARBAMOYL)-5,6-DIHYDROXYOCTA HYDRO-1H-INDOL-1-YL)-3-CHLORO-4-METHYL-1-OXOPENTAN-2-YLAMINO)-2-METHOXY-3-OXOPROPYL HYDROGEN SULFATE
C26 H43 Cl N6 O10 S
BVKDJAALSHFQTE-WNZJUFNWSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
D [auth H]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS		C [auth D]L-PEPTIDE LINKINGC9 H11 N O6 STYR
Binding Affinity Annotations 
IDSourceBinding Affinity
SN3 PDBBind:  2GDE IC50: 5.7 (nM) from 1 assay(s)
Binding MOAD:  2GDE IC50: 5.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.084α = 90
b = 72.169β = 99.06
c = 70.357γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CCP4data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2006-03-16 
  • Released Date: 2007-03-20 
    • Deposition Author(s): Xue, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    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: 2012-12-12
    Changes: Other
  • Version 1.4: 2013-03-13
    Changes: Other