SMTL ID : 7t1i.1

Crystal structure of CAB1 Pantothenate Kinase from Saccharomyces cerevisiae in complex with compound YU385597

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x E4C: (8S)-2-{[(4-tert-butylphenyl)methyl]amino}-5-[(piperidin-1-yl)methyl][1,2,4]triazolo[1,5-a]pyrimidin-7(6H)-one(Non-covalent)

E4C.1: 20 residues within 4Å: Chain A: E.113, M.114, V.168, S.169, R.181, G.183, G.184, S.185, S.186 Chain B: I.227, Y.228, Y.232, I.235, G.236, L.237, I.242, A.243, F.338, W.339 Ligands: EDO.7 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.227, B:Y.228, B:Y.232, B:Y.232, B:L.237, B:L.237, B:A.243, B:F.338, B:W.339 Hydrogen bonds: B:I.242, A:R.181, A:R.181 Water bridges: A:S.186 pi-Cation interactions: A:R.181 E4C.8: 20 residues within 4Å: Chain A: V.224, I.227, Y.228, Y.232, I.235, G.236, L.237, I.242, A.243, F.338, W.339 Chain B: M.114, V.168, S.169, R.181, G.183, G.184, S.185, S.186 Ligands: EDO.4 15 PLIP interactions: 4 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:R.181, B:R.181, A:I.242 Water bridges: B:S.186 pi-Cation interactions: B:R.181 Hydrophobic interactions: A:V.224, A:I.227, A:Y.228, A:Y.232, A:Y.232, A:L.237, A:L.237, A:A.243, A:F.338, A:W.339

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: G.34, G.35, T.36, L.37, K.39, G.165, S.166 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.35, A:T.36, A:L.37, A:L.37, A:S.166 Water bridges: A:G.167, A:G.167 Salt bridges: A:K.39 SO4.3: 3 residues within 4Å: Chain A: K.308, S.343, K.344 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.343 Salt bridges: A:K.308, A:K.344 SO4.9: 7 residues within 4Å: Chain B: G.34, G.35, T.36, L.37, G.165, S.166 Ligands: EDO.11 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.35, B:T.36, B:T.36, B:T.36, B:L.37, B:S.166 Water bridges: B:G.167, B:G.167 Salt bridges: B:K.39 SO4.10: 4 residues within 4Å: Chain B: G.77, C.78, Y.79, R.80 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.79, B:R.80 Salt bridges: B:R.80

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: N.297, Y.334, A.335, F.338, W.339 Ligands: E4C.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.339 Water bridges: A:N.297, A:Y.334 EDO.7: 5 residues within 4Å: Chain B: N.297, A.335, F.338, W.339 Ligands: E4C.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.339 EDO.11: 6 residues within 4Å: Chain B: L.37, K.39, G.319, S.320, G.353 Ligands: SO4.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.39, B:G.353 Water bridges: B:N.163, B:L.355

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 8 residues within 4Å: Chain A: Y.228, T.230, D.231, Y.232, K.234 Chain B: F.92, E.112, E.113 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.228, B:E.113 Water bridges: A:Y.228, A:N.233, B:T.87 PEG.6: 6 residues within 4Å: Chain A: F.92 Chain B: T.230, D.231, Y.232, N.233, K.234 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.230, B:N.233, B:K.234 Water bridges: B:N.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gihaz, S. et al., High-resolution crystal structure and chemical screening reveal pantothenate kinase as a new target for antifungal development. Structure (2022)

Release Date

2022-10-05

Peptides

Pantothenate kinase CAB1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pantothenate kinase CAB1

Related Entries With Identical Sequence