SMTL ID : 4pnz.1

Human dipeptidyl peptidase IV/CD26 in complex with the long-acting inhibitor Omarigliptin (MK-3102)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain A: N.181, T.183, F.184, N.234, Q.270, E.271, Y.292, E.294 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.184, A:Y.292 Hydrogen bonds: A:E.294, A:E.294 NAG-NAG.2: 5 residues within 4Å: Chain A: I.156, Q.189, N.191, T.193, E.194 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.193 NAG-NAG.3: 6 residues within 4Å: Chain A: I.281, N.283, S.311, T.312, R.558, D.640 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.640 NAG-NAG.4: 8 residues within 4Å: Chain B: N.181, T.183, F.184, N.234, Q.270, E.271, Y.292, E.294 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.184, B:Y.292 Hydrogen bonds: B:N.234 Water bridges: B:E.294, B:E.294 NAG-NAG.5: 4 residues within 4Å: Chain B: I.156, N.191, T.193, E.194 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.193

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

NA.6: 3 residues within 4Å: Chain A: G.452, L.453, R.454 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.452

2 x 2VH: (2R,3S,5R)-5-[2-(methylsulfonyl)-2,6-dihydropyrrolo[3,4-c]pyrazol-5(4H)-yl]-2-(2,4,5-trifluorophenyl)tetrahydro-2H-pyran-3-amine(Non-covalent)

2VH.7: 15 residues within 4Å: Chain A: R.87, E.167, E.168, S.171, F.319, Y.509, S.592, Y.593, V.618, W.621, Y.624, Y.628, N.672, V.673, H.702 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.673 Hydrogen bonds: A:E.167, A:E.168, A:S.171, A:Y.509, A:Y.624 Water bridges: A:R.87 pi-Stacking: A:F.319, A:Y.628 pi-Cation interactions: A:F.319 2VH.11: 14 residues within 4Å: Chain B: R.87, E.167, E.168, S.171, F.319, Y.509, S.592, Y.593, V.618, Y.624, Y.628, N.672, V.673, H.702 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.673 Hydrogen bonds: B:E.167, B:E.168, B:S.171 Water bridges: B:R.87, B:Y.509 pi-Stacking: B:F.319, B:Y.628 pi-Cation interactions: B:F.319 Halogen bonds: B:N.672

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

NAG.8: 6 residues within 4Å: Chain A: E.29, V.40, N.42, N.47, S.48, S.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.47 Water bridges: A:E.29, A:N.42 NAG.9: 4 residues within 4Å: Chain A: R.109, I.110, P.111, N.112 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.109 Water bridges: A:R.109, A:I.110, A:N.112 NAG.10: 3 residues within 4Å: Chain A: W.149, V.241, N.243 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.243, A:N.243 NAG.12: 5 residues within 4Å: Chain B: E.29, V.40, N.47, S.48, S.49 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.47 Water bridges: B:E.29, B:S.49, B:S.49 NAG.13: 4 residues within 4Å: Chain B: E.35, N.36, N.37, N.54 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.37 NAG.14: 3 residues within 4Å: Chain B: R.109, I.110, N.112 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.109 Hydrogen bonds: B:R.109 Water bridges: B:N.112 NAG.15: 2 residues within 4Å: Chain B: W.149, N.243 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.243 NAG.16: 5 residues within 4Å: Chain B: I.281, N.283, S.311, T.312, R.558 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.558

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biftu, T. et al., Omarigliptin (MK-3102): A Novel Long-Acting DPP-4 Inhibitor for Once-Weekly Treatment of Type 2 Diabetes. J.Med.Chem. (2014)

Release Date

2014-04-09

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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