9GCD | pdb_00009gcd

CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH Fulacimstat (COMPOUND86)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.212 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.178 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery and Preclinical Characterization of Fulacimstat (BAY 1142524), a Potent and Selective Chymase Inhibitor As a New Profibrinolytic Approach for Safe Thrombus Resolution.

Furstner, C.Ackerstaff, J.Meier, H.Straub, A.Mittendorf, J.Schamberger, J.Schafer, M.Borngen, K.Jorissen, H.Zubov, D.Zimmermann, K.Tersteegen, A.Geiss, V.Hartmann, E.Albrecht-Kupper, B.D'Orleans-Juste, P.Lapointe, C.Vincent, L.Heitmeier, S.Tinel, H.

(2025) J Med Chem 68: 6108-6126

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01819
  • Primary Citation Related Structures: 
    9GBH, 9GC1, 9GC9, 9GCC, 9GCD

  • PubMed Abstract: 

    Chymase is a serine-protease produced by mast cells. In the past few decades, its role in fibrotic diseases triggered the search for orally available chymase inhibitors. Aiming at reducing adverse cardiac remodeling after myocardial infarction, our research efforts resulted in the discovery of fulacimstat (BAY 1142524). While clinical trials did not demonstrate efficacy in this indication, the recent discovery of a new unexpected biological role of chymase spurred a revival of interest in chymase inhibition: chymase was shown to inactivate plasmin within fibrin-rich clots. Chymase inhibitors are now considered as potential profibrinolytic drugs with low bleeding risk and therefore exceptional safety for the treatment of acute thrombosis settings such as stroke, pulmonary embolism, or venous thrombosis. This article describes the chemical optimization journey from a screening hit to the discovery of fulacimstat (BAY 1142524), a selective chymase inhibitor with a good safety profile, as well as its preclinical in vitro and in vivo characterization.


  • Organizational Affiliation
    • Bayer AG, Pharmaceuticals, Research and Development, Aprather Weg 18a, 42113 Wuppertal, Germany.

Macromolecule Content 

  • Total Structure Weight: 26.75 kDa 
  • Atom Count: 2,032 
  • Modeled Residue Count: 215 
  • Deposited Residue Count: 226 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ChymaseA [auth AAA]226Homo sapiensMutation(s): 3 
Gene Names: CMA1CYHCYM
EC: 3.4.21.39
UniProt & NIH Common Fund Data Resources
Find proteins for P23946 (Homo sapiens)
Explore P23946 
Go to UniProtKB:  P23946
PHAROS:  P23946
GTEx:  ENSG00000092009 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23946
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P23946-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth AaA]4N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC
GlyCosmos: G22573RC
GlyGen: G22573RC
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth AbA]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IJ2
(Subject of Investigation/LOI)

Query on A1IJ2



Download:Ideal Coordinates CCD File
D [auth AAA]1-(3-methyl-2-oxidanylidene-1,3-benzoxazol-6-yl)-2,4-bis(oxidanylidene)-3-[(1R)-4-(trifluoromethyl)-2,3-dihydro-1H-inden-1-yl]pyrimidine-5-carboxylic acid
C23 H16 F3 N3 O6
JDARDSVOVYVQST-INIZCTEOSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth AAA]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.212 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.08α = 90
b = 74.08β = 90
c = 49.79γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references