Vanin-1 complexed with Compound 3

Experimental Data Snapshot

  • Resolution: 2.13 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Discovery of a Series of Pyrimidine Carboxamides as Inhibitors of Vanin-1.

Casimiro-Garcia, A.Allais, C.Brennan, A.Choi, C.Dower, G.Farley, K.A.Fleming, M.Flick, A.Frisbie, R.K.Hall, J.Hepworth, D.Jones, H.Knafels, J.D.Kortum, S.Lovering, F.E.Mathias, J.P.Mohan, S.Morgan, P.M.Parng, C.Parris, K.Pullen, N.Schlerman, F.Stansfield, J.Strohbach, J.W.Vajdos, F.F.Vincent, F.Wang, H.Wang, X.Webster, R.Wright, S.W.

(2022) J Med Chem 65: 757-784

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01849
  • Primary Citation of Related Structures:  
    7SLV, 7SLX, 7SLY

  • PubMed Abstract: 

    A diaryl ketone series was identified as vanin-1 inhibitors from a high-throughput screening campaign. While this novel scaffold provided valuable probe 2 that was used to build target confidence, concerns over the ketone moiety led to the replacement of this group. The successful replacement of this moiety was achieved with pyrimidine carboxamides derived from cyclic secondary amines that were extensively characterized using biophysical and crystallographic methods as competitive inhibitors of vanin-1. Through optimization of potency and physicochemical and ADME properties, and guided by co-crystal structures with vanin-1, 3 was identified with a suitable profile for advancement into preclinical development.

  • Organizational Affiliation

    Medicine Design, Pfizer Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pantetheinase482Homo sapiensMutation(s): 0 
Gene Names: VNN1
UniProt & NIH Common Fund Data Resources
Find proteins for O95497 (Homo sapiens)
Explore O95497 
Go to UniProtKB:  O95497
PHAROS:  O95497
GTEx:  ENSG00000112299 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95497
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G89225LT
GlyCosmos:  G89225LT
GlyGen:  G89225LT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth D]6N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G67849DJ
GlyCosmos:  G67849DJ
GlyGen:  G67849DJ
Experimental Data & Validation

Experimental Data

  • Resolution: 2.13 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.656α = 90
b = 111.511β = 90
c = 147.44γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2022-01-12 
  • Deposition Author(s): Vajdos, F.F.

Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-01-26
    Changes: Database references