2JH5

Human Thrombin Hirugen Inhibitor complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history. 


Literature

Sulfonamide-Related Conformational Effects and Their Importance in Structure-Based Design.

Senger, S., Chan, C., Convery, M.A., Hubbard, J.A., Shah, G.P., Watson, N.S., Young, R.J.

(2007) Bioorg Med Chem Lett 17: 2931

  • DOI: https://doi.org/10.1016/j.bmcl.2007.02.034
  • Primary Citation of Related Structures:  
    2JH0, 2JH5, 2JH6

  • PubMed Abstract: 

    Structure-based design (SBD) is a challenging endeavour since even localised SAR can hardly ever be explained by the variation of just one dominating factor. Here, we present a rare example where structural information combined with ab initio calculations clearly indicate that the observed difference in biological activity is dominated by conformational effects. The learnings discussed are successfully put to the test and have the potential to be of general use as a qualitative guide in SBD efforts.

    • Organizational Affiliation: 

    GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK. stefan.x.senger@gsk.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THROMBIN LIGHT CHAINA [auth C]36Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000180210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
THROMBIN HEAVY CHAINB [auth D]259Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000180210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HIRUDIN IIIAC [auth H]10Hirudo medicinalisMutation(s): 0 
UniProt
Find proteins for P28507 (Hirudo medicinalis)
Explore P28507 
Go to UniProtKB:  P28507
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28507
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
895
Query on 895
Download Ideal Coordinates CCD File 
F [auth D]2-(5-CHLORO-2-THIENYL)-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-OXOETHYL]-2-OXOPYRROLIDIN-3-YL}ETHENESULFONAMIDE
C17 H22 Cl N3 O5 S2
ACEFOQMQINFMRW-DYCFVMESSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA
Download Ideal Coordinates CCD File 
E [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS		C [auth H]L-PEPTIDE LINKINGC9 H11 N O6 STYR
Binding Affinity Annotations 
IDSourceBinding Affinity
895 PDBBind:  2JH5 Ki: 367 (nM) from 1 assay(s)
BindingDB:  2JH5 Ki: 367 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.363α = 90
b = 71.478β = 100.62
c = 72.106γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

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: 2007-05-08
    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: 2012-11-30
    Changes: Other
  • Version 1.3: 2013-03-13
    Changes: Other
  • Version 1.4: 2013-08-07
    Changes: Derived calculations, Other
  • Version 1.5: 2017-06-28
    Changes: Data collection
  • Version 1.6: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary