SMTL ID : 5eue.1

S1P Lyase Bacterial Surrogate bound to N-(2-((4-methoxy-2,5-dimethylbenzyl)amino)-1-phenylethyl)-5-methylisoxazole-3-carboxamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.83 Å

Oligo State

homo-dimer

Ligands

2 x 5S5: ~{N}-[(1~{S})-2-[(4-methoxy-2,5-dimethyl-phenyl)methylamino]-1-phenyl-ethyl]-5-methyl-1,2-oxazole-3-carboxamide(Non-covalent)

5S5.1: 14 residues within 4Å: Chain A: P.128, L.129, P.131, W.341, I.345, Y.346, A.347 Chain B: F.250, N.433, A.486, V.497, S.498, F.501, L.505 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.341, A:I.345, A:I.345, A:Y.346, B:F.250, B:A.486, B:F.501, B:L.505 Hydrogen bonds: A:L.129, A:A.347 5S5.4: 14 residues within 4Å: Chain A: F.250, M.479, V.482, V.497, F.501, L.505 Chain B: P.128, L.129, P.131, W.341, G.343, I.345, Y.346, A.347 13 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:F.250, A:F.250, A:V.482, A:F.501, A:L.505, B:L.129, B:L.129, B:W.341, B:I.345, B:A.347 Hydrogen bonds: B:L.129, B:A.347 pi-Stacking: B:Y.346

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

PO4.2: 10 residues within 4Å: Chain A: S.102, G.103, A.104, Y.106, K.312, K.318 Chain B: N.127, L.129, H.130, S.354 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.127, B:S.354, B:S.354, A:A.104 Salt bridges: B:H.130, A:K.318 PO4.3: 7 residues within 4Å: Chain A: N.127, L.129, H.130 Chain B: G.103, A.104, Y.106, K.312 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.104, B:Y.106, A:N.127 Salt bridges: B:K.318, A:H.130

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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