7SLY

Vanin-1 complexed with Compound 27

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

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 ...

    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., 445 Eastern Point Rd, Groton, Connecticut 06340, United States.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PantetheinaseA482Homo sapiensMutation(s): 0 
Gene Names: VNN1
EC: 3.5.1.92
UniProt & NIH Common Fund Data Resources
Find proteins for O95497 (Homo sapiens)
Explore O95497 
Go to UniProtKB:  O95497
PHAROS:  O95497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95497
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB 3N/AN-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D 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 Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G67849DJ
GlyCosmos:  G67849DJ
GlyGen:  G67849DJ
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9S5 (Subject of Investigation/LOI)
Query on 9S5
Download Ideal Coordinates CCD File 
E [auth A](8-oxa-2-azaspiro[4.5]decan-2-yl)(2-{[(1S)-1-(pyrazin-2-yl)ethyl]amino}pyrimidin-5-yl)methanone
C19 H24 N6 O2
RZEQDKIIEMKNMN-AWEZNQCLSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
D [auth A],
F [auth A]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.98α = 90
b = 110.973β = 90
c = 147.885γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALEPACKdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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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