7THS

Macrocyclic plasmin inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Synthesis and Structural Characterization of Macrocyclic Plasmin Inhibitors.

Wiedemeyer, S.J.A.Wu, G.Pham, T.L.P.Lang-Henkel, H.Perez Urzua, B.Whisstock, J.C.Law, R.H.P.Steinmetzer, T.

(2023) ChemMedChem 18: e202200632-e202200632

  • DOI: https://doi.org/10.1002/cmdc.202200632
  • Primary Citation of Related Structures:  
    7THS, 7UAH

  • PubMed Abstract: 

    Two series of macrocyclic plasmin inhibitors with a C-terminal benzylamine group were synthesized. The substitution of the N-terminal phenylsulfonyl group of a previously described inhibitor provided two analogues with sub-nanomolar inhibition constants. Both compounds possess a high selectivity against all other tested trypsin-like serine proteases. Furthermore, a new approach was used to selectively introduce asymmetric linker segments. Two of these compounds inhibit plasmin with K i values close to 2 nM. For the first time, four crystal structures of these macrocyclic inhibitors could be determined in complex with a Ser195Ala microplasmin mutant. The macrocyclic core segment of the inhibitors binds to the open active site of plasmin without any steric hindrance. This binding mode is incompatible with other trypsin-like serine proteases containing a sterically demanding 99-hairpin loop. The crystal structures obtained experimentally explain the excellent selectivity of this inhibitor type as previously hypothesized.


  • Organizational Affiliation

    Department of Pharmacy Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Plasminogen
A, B
250Homo sapiensMutation(s): 1 
Gene Names: PLG
EC: 3.4.21.7
UniProt & NIH Common Fund Data Resources
Find proteins for P00747 (Homo sapiens)
Explore P00747 
Go to UniProtKB:  P00747
PHAROS:  P00747
GTEx:  ENSG00000122194 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00747
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I5Y (Subject of Investigation/LOI)
Query on I5Y

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
(6S,9R,20R,23S)-N-{[4-(aminomethyl)phenyl]methyl}-20-[(benzenesulfonyl)amino]-3,13,21-trioxo-2,6,9,14,22-pentaazatetracyclo[23.2.2.2~6,9~.2~15,18~]tritriaconta-1(27),15,17,25,28,30-hexaene-23-carboxamide
C43 H52 N8 O6 S
IXYFBSOJHOQEEZ-ZESVVUHVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
I5Q
Query on I5Q

Download Ideal Coordinates CCD File 
L [auth B](2S)-butane-1,2-diol
C4 H10 O2
BMRWNKZVCUKKSR-BYPYZUCNSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.723α = 90
b = 50.598β = 93.04
c = 92.757γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-01-18 
  • Deposition Author(s): Guojie, W.

Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1127593

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-18
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Database references, Source and taxonomy
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description