SMTL ID : 5eud.1

S1P Lyase Bacterial Surrogate bound to N-(1-(4-(3-hydroxyprop-1-yn-1-yl)phenyl)-2-((4-methoxy-2,5-dimethylbenzyl)amino)ethyl)-5-methylisoxazole-3-carboxamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-dimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: G.103, A.104, Y.106, K.312 Chain B: N.127, L.129, H.130, S.354 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:N.127, A:A.104, A:Y.106 Water bridges: B:S.354, B:S.354, A:S.102, A:N.433 Salt bridges: B:H.130, A:K.318 PO4.4: 8 residues within 4Å: Chain A: N.127, L.129, H.130, S.354 Chain B: G.103, A.104, Y.106, K.312 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:A.104, A:N.127 Water bridges: B:A.104, B:Y.106, B:Y.106, B:K.318, B:N.433, B:N.433, A:H.130, A:S.354, A:S.354 Salt bridges: B:K.318, A:H.130

2 x 5S6: ~{N}-[(1~{S})-2-[(4-methoxy-2,5-dimethyl-phenyl)methylamino]-1-[4-(3-oxidanylprop-1-ynyl)phenyl]ethyl]-5-methyl-1,2-oxazole-3-carboxamide(Non-covalent)

5S6.2: 15 residues within 4Å: Chain A: H.202, F.250, K.312, A.486, V.497, F.501, L.505 Chain B: P.128, L.129, P.131, W.341, G.343, I.345, Y.346, A.347 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.250, A:F.250, A:F.250, A:A.486, A:L.505, B:L.129, B:W.341, B:I.345, B:Y.346 Hydrogen bonds: B:I.345, B:A.347 pi-Stacking: B:Y.346 5S6.3: 17 residues within 4Å: Chain A: P.128, L.129, P.131, W.341, G.343, I.345, Y.346, A.347 Chain B: H.202, F.250, K.312, V.482, A.486, V.497, S.498, F.501, L.505 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.129, A:W.341, A:W.341, A:I.345, A:Y.346, B:F.250, B:F.250, B:V.482, B:A.486, B:L.505 Hydrogen bonds: A:I.345, A:A.347 Water bridges: A:L.129 pi-Stacking: A:Y.346

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Argiriadi, M.A. et al., Creation of a S1P Lyase bacterial surrogate for structure-based drug design. Bioorg.Med.Chem.Lett. (2016)

Release Date

2016-03-16

Peptides

Putative sphingosine-1-phosphate lyase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative sphingosine-1-phosphate lyase

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