SMTL ID : 4jkv.1

Structure of the human smoothened 7TM receptor in complex with an antitumor agent

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x 1KS: 4-fluoro-N-methyl-N-{1-[4-(1-methyl-1H-pyrazol-5-yl)phthalazin-1-yl]piperidin-4-yl}-2-(trifluoromethyl)benzamide(Non-covalent)

1KS.1: 21 residues within 4Å: Chain A: N.139, L.141, M.150, W.201, M.221, D.304, V.306, S.307, I.309, F.311, Y.314, K.315, R.320, Q.397, W.400, E.401, F.404, P.433, E.438, N.441, L.442 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.201, A:V.306, A:P.433, A:E.438, A:L.442 Hydrogen bonds: A:N.139, A:Y.314, A:R.320, A:R.320 pi-Stacking: A:W.201, A:F.311, A:H.390, A:F.404 Halogen bonds: A:K.315 1KS.10: 22 residues within 4Å: Chain B: N.139, L.141, F.142, M.150, W.201, M.221, D.304, V.306, S.307, I.309, F.311, Y.314, K.315, R.320, Q.397, W.400, E.401, F.404, P.433, E.438, N.441, L.442 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.201, B:V.306, B:P.433, B:E.438, B:L.442 Hydrogen bonds: B:N.139, B:R.320, B:R.320 pi-Stacking: B:W.201, B:F.404 pi-Cation interactions: B:H.390 Halogen bonds: B:K.315

5 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.2: 7 residues within 4Å: Chain A: E.367, R.371, I.374, F.375, L.378, A.451, T.454 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.375, A:A.451 Hydrogen bonds: A:R.371 Salt bridges: A:R.371 OLC.3: 9 residues within 4Å: Chain A: Y.317, R.318, A.321, L.325, A.326, G.329, L.330, F.394 Chain B: A.297 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.325 Hydrogen bonds: A:Y.317, A:Y.317, A:R.318, B:A.297 OLC.4: 5 residues within 4Å: Chain A: S.388, F.391, Y.392, F.395, N.396 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.391 Hydrogen bonds: A:N.396 OLC.11: 8 residues within 4Å: Chain B: D.207, G.208, A.209, E.212, I.213, S.233, I.237, I.240 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.237, B:I.240 Hydrogen bonds: B:D.207 Water bridges: B:S.233 OLC.12: 4 residues within 4Å: Chain B: Y.153, L.436, K.439, F.443 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.439, B:F.443, B:F.443, B:F.443 Salt bridges: B:K.439

3 x OLA: OLEIC ACID(Non-covalent)

OLA.5: 11 residues within 4Å: Chain A: I.199, L.202, A.203, M.206, D.207, G.208, A.209, E.212, I.236, I.237, I.240 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.202, A:A.203, A:A.209, A:E.212, A:I.236, A:I.237, A:I.240 OLA.6: 4 residues within 4Å: Chain A: V.239, Y.243, H.281, W.285 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.239, A:Y.243, A:Y.243, A:W.285 Salt bridges: A:H.281 OLA.13: 4 residues within 4Å: Chain A: L.282 Chain B: I.333, Y.337, F.338 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.282, B:Y.337, B:Y.337, B:F.338 Hydrogen bonds: B:Y.337, B:Y.337

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

PEG.7: 6 residues within 4Å: Chain A: P.140, L.141, F.142, T.143, I.429, R.432 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.432 PEG.14: 4 residues within 4Å: Chain B: E.212, T.231, L.232, S.233 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.212, B:E.212, B:L.232 Water bridges: B:S.233

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 5 residues within 4Å: Chain A: Q.300, N.316, Y.319 Chain B: N.316, Y.319 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.318, B:Q.300

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 4 residues within 4Å: Chain A: D.149, Y.153, L.436, K.439 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.439

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, C. et al., Structure of the human smoothened receptor bound to an antitumour agent. Nature (2013)

Release Date

2013-04-24

Peptides

Soluble cytochrome b562, Smoothened homolog: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Soluble cytochrome b562, Smoothened homolog

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