SMTL ID : 7sly.1

Vanin-1 complexed with Compound 27

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: N.314, T.316, S.320 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA- BMA- BMA: 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-glucopyranose

NAG-NAG-BMA-BMA-BMA-BMA.2: 2 residues within 4Å: Chain A: N.199, H.306 No protein-ligand interaction detected (PLIP)

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 2 residues within 4Å: Chain A: C.125, N.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.129 NAG.5: 3 residues within 4Å: Chain A: A.350, G.351, N.352 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.350 Hydrogen bonds: A:N.352

1 x 9S5: (8-oxa-2-azaspiro[4.5]decan-2-yl)(2-{[(1S)-1-(pyrazin-2-yl)ethyl]amino}pyrimidin-5-yl)methanone(Non-covalent)

9S5.4: 20 residues within 4Å: Chain A: E.78, D.79, W.84, K.177, F.181, E.184, C.210, F.211, L.214, A.236, W.237, M.238, V.240, L.244, K.271, M.273, F.337, V.388, E.389, Y.392 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.84, A:F.181, A:F.181, A:W.237, A:V.240, A:L.244 Hydrogen bonds: A:K.177, A:F.211, A:M.238, A:M.238 pi-Stacking: A:F.181, A:W.237, A:F.337

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Casimiro-Garcia, A. et al., Discovery of a Series of Pyrimidine Carboxamides as Inhibitors of Vanin-1. J.Med.Chem. (2022)

Release Date

2022-01-12

Peptides

Pantetheinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pantetheinase

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