SMTL ID : 2onc.1 (2 other biounits)

Crystal structure of human DPP-4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain A: W.152, N.246 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: I.159, Q.192, N.194, T.196, E.197, K.232 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: I.159, N.194, T.196, E.197 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: N.50, S.51 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.50, A:S.51 NAG.5: 2 residues within 4Å: Chain A: I.113, N.115 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain A: N.184, T.186, Q.273, E.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.184, A:E.274, A:E.274 NAG.7: 5 residues within 4Å: Chain A: I.284, N.286, M.313, S.314, R.561 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.561 NAG.10: 2 residues within 4Å: Chain B: Y.48, N.50 No protein-ligand interaction detected (PLIP) NAG.11: 2 residues within 4Å: Chain B: I.113, N.115 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.115, B:N.115 NAG.12: 4 residues within 4Å: Chain B: N.184, T.186, Q.273, E.274 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.274 Water bridges: B:T.186 NAG.13: 2 residues within 4Å: Chain B: W.152, N.246 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.246

4 x SY1: 2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]-4-OXOQUINAZOLIN-3(4H)-YL}METHYL)BENZONITRILE(Non-covalent)

SY1.8: 14 residues within 4Å: Chain A: R.90, E.170, E.171, F.322, Y.512, W.594, S.595, Y.596, V.621, Y.627, Y.631, N.675, V.676, H.705 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.322, A:Y.596, A:V.621, A:Y.627, A:V.676 Hydrogen bonds: A:R.90, A:E.170, A:Y.512, A:Y.596 Water bridges: A:Y.627, A:Y.627 pi-Stacking: A:Y.512, A:Y.631 SY1.9: 9 residues within 4Å: Chain A: Q.88, E.156, D.157, F.205, K.215, T.216, V.217, R.218, V.219 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.215, A:K.215, A:V.217 Hydrogen bonds: A:K.215, A:R.218, A:R.218 Water bridges: A:Q.88 pi-Stacking: A:F.205 pi-Cation interactions: A:K.215 SY1.14: 14 residues within 4Å: Chain B: R.90, E.170, E.171, F.322, Y.512, W.594, S.595, Y.596, V.621, Y.627, Y.631, N.675, V.676, H.705 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.322, B:Y.596, B:V.621, B:Y.627, B:Y.627, B:V.676 Hydrogen bonds: B:R.90, B:E.170, B:Y.596 pi-Stacking: B:Y.512, B:Y.631 SY1.15: 9 residues within 4Å: Chain B: Q.88, E.156, D.157, F.205, K.215, T.216, V.217, R.218, V.219 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.217, B:V.217 Hydrogen bonds: B:Q.88, B:K.215, B:R.218, B:R.218 pi-Stacking: B:F.205 pi-Cation interactions: B:K.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, J. et al., Discovery of alogliptin: a potent, selective, bioavailable, and efficacious inhibitor of dipeptidyl peptidase IV. J.Med.Chem. (2007)

Release Date

2008-03-04

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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