SMTL ID : 6zpl.1

Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor, sybody Sb_GlyT1#7 and bound Na and Cl ions.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.95 Å

Oligo State

hetero-2-1-2-mer

Ligands

2 x QET: [5-fluoranyl-6-(oxan-4-yloxy)-1,3-dihydroisoindol-2-yl]-[5-methylsulfonyl-2-[2,2,3,3,3-pentakis(fluoranyl)propoxy]phenyl]methanone(Non-covalent)

QET.1: 27 residues within 4Å: Chain A: Y.25, A.26, V.27, G.28, L.29, G.30, N.31, F.63, L.67, Y.105, Y.262, S.263, L.264, G.265, W.268, G.270, L.271, M.274, A.275, N.278, D.287, I.291, N.295, T.364, C.367, L.368, T.371 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.25, A:L.67, A:W.268, A:L.271, A:T.364 Hydrogen bonds: A:T.364 pi-Stacking: A:Y.25 Halogen bonds: A:T.364 QET.4: 26 residues within 4Å: Chain B: Y.25, A.26, V.27, G.28, G.30, N.31, F.63, L.67, Y.262, S.263, L.264, G.265, W.268, G.270, L.271, M.274, A.275, N.278, D.287, I.291, N.295, T.364, C.367, L.368, T.371 Ligands: NA.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.25, B:Y.25, B:L.67, B:W.268, B:L.271, B:T.364 Hydrogen bonds: B:T.364 pi-Stacking: B:Y.25 Halogen bonds: B:T.364, B:C.367, B:T.371

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: G.24, Y.25, V.27, L.360 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.27 NA.5: 6 residues within 4Å: Chain B: G.24, Y.25, V.27, G.28, T.364 Ligands: QET.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.27, B:T.364

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 7 residues within 4Å: Chain A: N.31, F.35, Y.51, Q.259, S.263, N.295, S.299 Ligand excluded by PLIP CL.6: 7 residues within 4Å: Chain B: N.31, F.35, Y.51, Q.259, S.263, N.295, S.299 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shahsavar, A. et al., Structural insights into the inhibition of glycine reuptake. Nature (2021)

Release Date

2021-03-17

Peptides

Sodium- and chloride-dependent glycine transporter 1: AB
Endoglucanase H: C
Sybody Sb_GlyT1#7: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
E

E
F

Membrane

We predict this structure to be a membrane protein.
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Sodium- and chloride-dependent glycine transporter 1

Endoglucanase H

Sybody Sb_GlyT1#7

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