SMTL ID : 3wqh.1

Crystal Structure of human DPP-IV in complex with Anagliptin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-dimer

Ligands

13 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG.1: 5 residues within 4Å: Chain A: V.42, N.44, N.49, S.50, S.51 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.42 Hydrogen bonds: A:N.44, A:N.49 NAG.2: 3 residues within 4Å: Chain A: H.64, N.83, N.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.64, A:N.83 NAG.3: 4 residues within 4Å: Chain A: N.183, T.185, Q.272, E.273 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.183, A:T.185, A:T.185, A:E.273 NAG.4: 7 residues within 4Å: Chain A: I.158, Q.191, N.193, T.195, E.196, K.231 Ligands: NAG.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.158 Hydrogen bonds: A:N.193, A:E.196 NAG.5: 2 residues within 4Å: Chain A: W.151, N.245 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.245 NAG.6: 5 residues within 4Å: Chain A: I.283, N.285, M.312, S.313, R.560 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.313, A:R.560 Water bridges: A:N.285 NAG.7: 1 residues within 4Å: Ligands: NAG.4 No protein-ligand interaction detected (PLIP) NAG.9: 5 residues within 4Å: Chain B: E.31, V.42, N.49, S.50, S.51 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.42 Hydrogen bonds: B:N.49 NAG.10: 9 residues within 4Å: Chain B: H.64, Y.82, N.83, S.95, Y.96, D.97, R.111, I.112, N.114 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.82, B:Y.82, B:Y.82, B:R.111, B:N.114 NAG.11: 4 residues within 4Å: Chain B: N.183, T.185, Q.272, E.273 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.183, B:T.185, B:E.273, B:E.273 Water bridges: B:E.296 NAG.12: 7 residues within 4Å: Chain B: T.152, I.158, Q.191, N.193, T.195, E.196, K.231 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.158 Hydrogen bonds: B:N.193, B:T.195, B:E.196, B:E.196, B:K.231 NAG.13: 3 residues within 4Å: Chain B: W.151, V.243, N.245 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.243 NAG.14: 5 residues within 4Å: Chain B: I.283, N.285, M.312, S.313, R.560 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.560

2 x SKK: N-[2-({2-[(2S)-2-cyanopyrrolidin-1-yl]-2-oxoethyl}amino)-2-methylpropyl]-2-methylpyrazolo[1,5-a]pyrimidine-6-carboxamide(Non-covalent)

SKK.8: 13 residues within 4Å: Chain A: R.89, E.169, E.170, S.173, F.321, Y.511, Y.549, S.594, Y.595, Y.626, Y.630, N.674, H.704 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.626, A:Y.630, A:Y.630 Hydrogen bonds: A:R.89, A:E.169, A:E.169, A:S.594, A:N.674 pi-Stacking: A:F.321 SKK.15: 14 residues within 4Å: Chain B: R.89, E.169, E.170, S.173, F.321, R.322, Y.511, Y.549, S.594, Y.595, Y.626, Y.630, N.674, H.704 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.626, B:Y.630 Hydrogen bonds: B:R.89, B:E.169, B:R.322, B:R.322, B:Y.511, B:S.594, B:N.674 pi-Stacking: B:F.321

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, Y.S. et al., Anagliptin, a potent dipeptidyl peptidase IV inhibitor: its single-crystal structure and enzyme interactions. J Enzyme Inhib Med Chem (2015)

Release Date

2015-07-15

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4