SMTL ID : 7w47.1

Crystal structure of the gastric proton pump complexed with tegoprazan

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: S.226, D.386, T.388, D.727, N.730 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.388, A:D.727

3 x RB: RUBIDIUM ION(Non-covalent)

RB.2: 6 residues within 4Å: Chain A: A.340, V.342, E.344, N.793, E.796, E.821 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:A.340, A:E.344, A:E.821 RB.3: 5 residues within 4Å: Chain A: N.289, L.735, K.736, A.738, D.757 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:K.736, A:A.738, A:D.757 RB.4: 3 residues within 4Å: Chain A: S.409, Q.419, T.420 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.409, A:T.420

1 x 8BN: Tegoprazan(Non-covalent)

8BN.5: 16 residues within 4Å: Chain A: I.120, A.124, Q.128, D.138, N.139, L.142, V.332, M.335, A.336, A.340, E.796, Y.800, L.810, L.812, G.813, C.814 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.124, A:D.138, A:A.336, A:A.340, A:Y.800, A:Y.800 Hydrogen bonds: A:L.812, A:C.814 Water bridges: A:Y.929 Halogen bonds: A:Y.800

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 5 residues within 4Å: Chain B: N.99, S.101, N.255, Q.289, K.290 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.289 Hydrogen bonds: B:K.290 NAG.7: 1 residues within 4Å: Chain B: N.130 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain B: N.161, E.216, F.218 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.216, B:F.218 Hydrogen bonds: B:E.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, S. et al., Structural Basis for Binding of Potassium-Competitive Acid Blockers to the Gastric Proton Pump. J.Med.Chem. (2022)

Release Date

2022-01-05

Peptides

Potassium-transporting ATPase alpha chain 1: A
Potassium-transporting ATPase subunit beta: B

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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Potassium-transporting ATPase alpha chain 1

Potassium-transporting ATPase subunit beta

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