SMTL ID : 3w2t.1

Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with vildagliptin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-dimer

Ligands

2 x NAG- FUL: beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUL.1: 5 residues within 4Å: Chain A: V.46, Y.51, N.53, S.54, S.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.53 NAG-FUL.5: 7 residues within 4Å: Chain B: E.35, V.46, N.48, Y.51, N.53, S.54, S.55 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.51, B:N.48 Water bridges: B:N.53, B:S.54

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

NAG-NAG.2: 8 residues within 4Å: Chain A: N.187, T.189, F.190, N.240, Q.276, E.277, Y.298, E.300 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.190, A:Y.298 Hydrogen bonds: A:N.240, A:E.300, A:E.300 Water bridges: A:T.189 NAG-NAG.3: 3 residues within 4Å: Chain A: W.155, T.156, N.249 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.156 NAG-NAG.4: 8 residues within 4Å: Chain A: I.287, N.289, M.316, S.317, T.318, R.564, D.646 Ligands: GOL.10 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 8 residues within 4Å: Chain B: N.187, T.189, F.190, N.240, Q.276, E.277, Y.298, E.300 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.190, B:Y.298 Hydrogen bonds: B:N.240 NAG-NAG.7: 5 residues within 4Å: Chain B: I.162, N.197, T.199, E.200, K.235 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 8 residues within 4Å: Chain B: I.287, N.289, M.316, S.317, T.318, R.564, D.646 Ligands: GOL.15 No protein-ligand interaction detected (PLIP)

2 x LF7: 2-{[(1r,3s,5R,7S)-3-hydroxytricyclo[3.3.1.1~3,7~]decan-1-yl]amino}-1-{(2S)-2-[(E)-iminomethyl]pyrrolidin-1-yl}ethan-1-o ne(Covalent)

LF7.9: 13 residues within 4Å: Chain A: R.93, E.173, E.174, F.325, Y.515, S.598, Y.599, V.624, Y.630, Y.634, N.678, V.679, H.708 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.325, A:Y.599, A:V.624, A:Y.630, A:Y.630, A:Y.634, A:V.679 Hydrogen bonds: A:R.93, A:E.173, A:E.173, A:Y.515, A:Y.515, A:Y.599, A:N.678 LF7.14: 13 residues within 4Å: Chain B: R.93, E.173, E.174, F.325, Y.515, S.598, Y.599, V.624, Y.630, Y.634, N.678, V.679, H.708 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.325, B:V.624, B:Y.630, B:Y.630, B:Y.634, B:V.679 Hydrogen bonds: B:R.93, B:E.173, B:E.173, B:Y.515, B:Y.599, B:Y.630, B:N.678

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 9 residues within 4Å: Chain A: Q.288, N.289, G.320, W.321, N.563, R.564, R.637, G.640 Ligands: NAG-NAG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.288, A:Q.288, A:N.289, A:N.563, A:R.564 GOL.15: 10 residues within 4Å: Chain B: Q.288, N.289, G.320, W.321, N.563, R.564, E.636, R.637, G.640 Ligands: NAG-NAG.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.288, B:Q.288, B:N.563, B:R.564 Water bridges: B:N.289, B:D.646

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

NAG.11: 4 residues within 4Å: Chain A: E.41, N.42, N.43, N.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.42, A:N.43, A:N.60 NAG.12: 3 residues within 4Å: Chain A: R.115, I.116, N.118 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.115 Hydrogen bonds: A:R.115, A:R.115 NAG.13: 4 residues within 4Å: Chain A: I.162, N.197, T.199, E.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.199, A:E.200 Water bridges: A:N.197 NAG.16: 3 residues within 4Å: Chain B: R.115, I.116, N.118 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.115 Hydrogen bonds: B:R.115 Water bridges: B:N.118 NAG.17: 3 residues within 4Å: Chain B: W.155, V.247, N.249 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nabeno, M. et al., A comparative study of the binding modes of recently launched dipeptidyl peptidase IV inhibitors in the active site. Biochem.Biophys.Res.Commun. (2013)

Release Date

2013-05-15

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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