7SLX

Vanin-1 complexed with Compound 11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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.

(2021) J Med Chem 

  • DOI: 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
Find similar proteins by:  (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
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

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-glucopyranoseB3N/AN-Glycosylation Oligosaccharides Interaction
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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9SS
Query on 9SS

Download Ideal Coordinates CCD File 
E [auth A](3R)-1-(2-{[1-(pyrimidin-5-yl)cyclopropyl]amino}pyrimidine-5-carbonyl)piperidine-3-carbonitrile
C18 H19 N7 O
CDTXEVWHMGPGKZ-ZDUSSCGKSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
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
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
AL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.55α = 90
b = 111.83β = 90
c = 147.53γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2021-10-25 
  • 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