8RIJ | pdb_00008rij

Discovery of the first orally bioavailable ADAMTS7 inhibitor BAY-9835


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.219 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8RIJ

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

BAY-9835: Discovery of the First Orally Bioavailable ADAMTS7 Inhibitor.

Meibom, D.Wasnaire, P.Beyer, K.Broehl, A.Cancho-Grande, Y.Elowe, N.Henninger, K.Johannes, S.Jungmann, N.Krainz, T.Lindner, N.Maassen, S.MacDonald, B.Menshykau, D.Mittendorf, J.Sanchez, G.Schaefer, M.Stefan, E.Torge, A.Xing, Y.Zubov, D.

(2024) J Med Chem 67: 2907-2940

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02036
  • Primary Citation Related Structures: 
    8RIJ

  • PubMed Abstract: 

    The matrix metalloprotease ADAMTS7 has been identified by multiple genome-wide association studies as being involved in the development of coronary artery disease. Subsequent research revealed the proteolytic function of the enzyme to be relevant for atherogenesis and restenosis after vessel injury. Based on a publicly known dual ADAMTS4/ADAMTS5 inhibitor, we have in silico designed an ADAMTS7 inhibitor of the catalytic domain, which served as a starting point for an optimization campaign. Initially our inhibitors suffered from low selectivity vs MMP12. An X-ray cocrystal structure inspired us to exploit amino acid differences in the binding site of MMP12 and ADAMTS7 to improve selectivity. Further optimization composed of employing 5-membered heteroaromatic groups as hydantoin substituents to become more potent on ADAMTS7. Finally, fine-tuning of DMPK properties yielded BAY-9835, the first orally bioavailable ADAMTS7 inhibitor. Further optimization to improve selectivity vs ADAMTS12 seems possible, and a respective starting point could be identified.


  • Organizational Affiliation
    • Bayer AG, 42113 Wuppertal, Germany.

Macromolecule Content 

  • Total Structure Weight: 18.24 kDa 
  • Atom Count: 1,403 
  • Modeled Residue Count: 158 
  • Deposited Residue Count: 158 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Macrophage metalloelastase158Homo sapiensMutation(s): 1 
Gene Names: MMP12HME
EC: 3.4.24.65
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens)
Explore P39900 
Go to UniProtKB:  P39900
PHAROS:  P39900
GTEx:  ENSG00000262406 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39900
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H07
(Subject of Investigation/LOI)

Query on A1H07



Download:Ideal Coordinates CCD File
G [auth A]~{N}-[[(4~{R})-4-cyclopropyl-2,5-bis(oxidanylidene)imidazolidin-4-yl]methyl]-2-(3-fluorophenyl)-1,2,3-triazole-4-carboxamide
C16 H15 F N6 O3
ISBGRIYURXSYTK-INIZCTEOSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
H [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.219 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.245α = 90
b = 62.986β = 90
c = 59.477γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references
  • Version 1.2: 2025-07-02
    Changes: Refinement description, Structure summary