6T9V

Bovine Trypsin in complex with the synthetic inhibitor (S)-3-(3-(4-(3-(tert-butyl)ureido)piperidin-1-yl)-2-((3'-fluoro-4'-(hydroxymethyl)-[1,1'-biphenyl])-3-sulfonamido)-3-oxopropyl)benzimidamide (MI-1904)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history


Literature

Improving the selectivity of 3-amidinophenylalanine-derived matriptase inhibitors

Pilgram, O.Keils, A.Benary, G.E.Muller, J.Merkl, S.Ngaha, S.Huber, S.Chevillard, F.Harbig, A.Magdolen, V.Heine, A.Bottcher-Friebertshauser, E.Steinmetzer, T.

(2022) Eur J Med Chem : 114437


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cationic Trypsin246Bos taurusMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00760
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MXH (Subject of Investigation/LOI)
Query on MXH

Download Ideal Coordinates CCD File 
F [auth A]1-~{tert}-butyl-3-[1-[(2~{S})-3-(3-carbamimidoylphenyl)-2-[[3-[3-fluoranyl-4-(hydroxymethyl)phenyl]phenyl]sulfonylamino ]propanoyl]piperidin-4-yl]urea
C33 H41 F N6 O5 S
FQLCVDCDDCIBQS-LJAQVGFWSA-N
TFA
Query on TFA

Download Ideal Coordinates CCD File 
B [auth A]trifluoroacetic acid
C2 H F3 O2
DTQVDTLACAAQTR-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.464α = 90
b = 55.464β = 90
c = 109.142γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 2.0: 2021-07-07
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2022-06-01
    Changes: Database references
  • Version 2.2: 2024-01-24
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-11-20
    Changes: Structure summary