6BTN

BMP1 complexed with a reverse hydroxymate - compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Reverse Hydroxamate Inhibitors of Bone Morphogenetic Protein 1.

Kallander, L.S.Washburn, D.Hilfiker, M.A.Eidam, H.S.Lawhorn, B.G.Prendergast, J.Fox, R.Dowdell, S.Manns, S.Hoang, T.Zhao, S.Ye, G.Hammond, M.Holt, D.A.Roethke, T.Hong, X.Reid, R.A.Gampe, R.Zhang, H.Diaz, E.Rendina, A.R.Quinn, A.M.Willette, B.

(2018) ACS Med Chem Lett 9: 736-740

  • DOI: 10.1021/acsmedchemlett.8b00173
  • Primary Citation of Related Structures:  
    6BSL, 6BSM, 6BTQ, 6BTP, 6BTO, 6BTN

  • PubMed Abstract: 
  • Bone Morphogenetic Protein 1 (BMP1) inhibition is a potential method for treating fibrosis because BMP1, a member of the zinc metalloprotease family, is required to convert pro-collagen to collagen. A novel class of reverse hydroxamate BMP1 inhibitors was discovered, and cocrystal structures with BMP1 were obtained ...

    Bone Morphogenetic Protein 1 (BMP1) inhibition is a potential method for treating fibrosis because BMP1, a member of the zinc metalloprotease family, is required to convert pro-collagen to collagen. A novel class of reverse hydroxamate BMP1 inhibitors was discovered, and cocrystal structures with BMP1 were obtained. The observed binding mode is unique in that the small molecule occupies the nonprime side of the metalloprotease pocket providing an opportunity to build in metalloprotease selectivity. Structure-guided modification of the initial hit led to the identification of an oral in vivo tool compound with selectivity over other metalloproteases. Due to irreversible inhibition of cytochrome P450 3A4 for this chemical class, the risk of potential drug-drug interactions was managed by optimizing the series for subcutaneous injection.


    Organizational Affiliation

    Heart Failure Discovery Performance Unit, Metabolic Pathways and Cardiovascular Therapeutic Area, and Platform Technology and Sciences, GlaxoSmithKline Pharmaceuticals, King of Prussia, Pennsylvania 19406, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bone morphogenetic protein 1A, B202Homo sapiensMutation(s): 1 
Gene Names: BMP1PCOLC
EC: 3.4.24.19
UniProt & NIH Common Fund Data Resources
Find proteins for P13497 (Homo sapiens)
Explore P13497 
Go to UniProtKB:  P13497
PHAROS:  P13497
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E8M (Subject of Investigation/LOI)
Query on E8M

Download Ideal Coordinates CCD File 
F [auth A](3S)-6-cyclohexyl-3-{3-[(dimethylamino)methyl]-1,2,4-oxadiazol-5-yl}-N-hydroxyhexanamide
C17 H30 N4 O3
ILYORWQDLYKJJF-AWEZNQCLSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], G [auth B], H [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.69α = 90
b = 90.239β = 90
c = 124.4γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release