1YPJ

Thrombin Inhibitor Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.239 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UIBClick on this verticalbar to view details

This is version 1.7 of the entry. See complete history


Literature

A simple protocol to estimate differences in protein binding affinity for enantiomers without prior resolution of racemates

Fokkens, J.Klebe, G.

(2006) Angew Chem Int Ed Engl 45: 985-989


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombin light chainA [auth L]27Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombin heavy chainB [auth H]257Homo 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

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HirudinC [auth I]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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UIB
Query on UIB

Download Ideal Coordinates CCD File 
D [auth H](1R,3AS,4R,8AS,8BR)-4-{5-(PHENYL[1,3]DIOXOL-5-YLMETHYL)-4-ETHYL-2,3,3-TRIMETHYL-6-OXO-OCTAHYDRO-PYRROLO[3,4-C]PYRROL-1-YL}-BENZAMIDINE
C26 H32 N4 O3
HQVPEQYGMUJQHM-MSYGRNIXSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
C [auth I]L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.239 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.521α = 90
b = 71.809β = 99.87
c = 71.308γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UIBClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    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
  • Version 1.5: 2013-11-13
    Changes: Other
  • Version 1.6: 2017-10-11
    Changes: Refinement description
  • Version 1.7: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary