SMTL ID : 4q6r.1

Crystal structure of human sphingosine-1-phosphate lyase in complex with inhibitor 6-[(2R)-4-(4-benzyl-7-chlorophthalazin-1-yl)-2-methylpiperazin-1-yl]pyridine-3-carbonitrile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.1: 11 residues within 4Å: Chain A: T.91, Y.93, H.185, F.233, K.296 Chain B: N.114, L.116, H.117, Y.330, S.338 Ligands: 30J.5 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.233, B:L.116 Hydrogen bonds: A:T.91, A:Y.93, B:N.114, B:S.338, B:S.338 Salt bridges: A:H.185, B:H.117

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.405, N.408, I.454, K.461, T.462, T.463 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.405, A:N.408, A:K.461, A:T.463

2 x 30J: 6-[(2R)-4-(4-benzyl-7-chlorophthalazin-1-yl)-2-methylpiperazin-1-yl]pyridine-3-carbonitrile(Non-covalent)

30J.3: 15 residues within 4Å: Chain A: L.116, P.118, D.119, G.327, I.329, Y.330, A.331 Chain B: I.468, Y.469, M.471, A.472, V.481, L.484, S.485, F.488 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.116, A:L.116, A:I.329, A:Y.330, B:I.468, B:F.488, B:F.488, B:F.488 Hydrogen bonds: A:A.331 30J.5: 15 residues within 4Å: Chain A: I.468, Y.469, A.472, V.481, L.484, S.485, F.488 Chain B: L.116, P.118, D.119, G.327, I.329, Y.330, A.331 Ligands: SIN.1 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.468, A:F.488, A:F.488, A:F.488, B:L.116, B:L.116, B:I.329, B:Y.330 Hydrogen bonds: B:A.331

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

PO4.4: 7 residues within 4Å: Chain A: N.114, L.116, H.117 Chain B: G.90, T.91, Y.93, K.296 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.91, B:Y.93, A:N.114 Salt bridges: A:H.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weiler, S. et al., Orally Active 7-Substituted (4-Benzylphthalazin-1-yl)-2-methylpiperazin-1-yl]nicotinonitriles as Active-Site Inhibitors of Sphingosine 1-Phosphate Lyase for the Treatment of Multiple Sclerosis. J.Med.Chem. (2014)

Release Date

2014-05-21

Peptides

Sphingosine-1-phosphate lyase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sphingosine-1-phosphate lyase 1