SMTL ID : 3nox.1

Crystal structure of human DPP-IV in complex with Sa-(+)-(6-(aminomethyl)-5-(2,4-dichlorophenyl)-7-methylimidazo[1,2-a]pyrimidin-2-yl)(morpholino)methanone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-dimer

Ligands

2 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: 6 residues within 4Å: Chain A: I.158, Q.191, N.193, T.195, E.196, K.231 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.195 NAG-NAG.2: 4 residues within 4Å: Chain B: I.158, N.193, T.195, E.196 No protein-ligand interaction detected (PLIP)

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

NAG.3: 6 residues within 4Å: Chain A: V.42, F.43, N.44, N.49, S.50, S.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.49 NAG.4: 4 residues within 4Å: Chain A: R.111, I.112, P.113, N.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.111, A:N.114 NAG.5: 7 residues within 4Å: Chain A: N.183, T.185, F.186, D.238, Q.272, E.273, E.296 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.185, A:T.185, A:E.273, A:E.296 NAG.6: 2 residues within 4Å: Chain A: W.151, N.245 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.245 NAG.7: 5 residues within 4Å: Chain A: L.483, N.484, R.545, E.568, D.569 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.483 Hydrogen bonds: A:N.484, A:R.545, A:R.545 NAG.9: 5 residues within 4Å: Chain B: V.42, N.44, N.49, S.50, S.51 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.42 Hydrogen bonds: B:N.49 Water bridges: B:E.31, B:N.44 NAG.10: 3 residues within 4Å: Chain B: E.37, N.39, N.56 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.37, B:N.39 NAG.11: 2 residues within 4Å: Chain B: R.111, N.114 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.111 Hydrogen bonds: B:N.114, B:N.114 Water bridges: B:R.111, B:N.114 NAG.12: 4 residues within 4Å: Chain B: N.183, T.185, Q.272, E.273 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.185, B:E.273 Water bridges: B:D.238 NAG.13: 5 residues within 4Å: Chain B: L.483, N.484, F.488, R.545, E.568 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.488 Hydrogen bonds: B:R.545, B:R.545, B:E.568 Water bridges: B:N.484, B:N.484

2 x 6A5: Sa-(+)-(6-(aminomethyl)-5-(2,4-dichlorophenyl)-7-methylimidazo[1,2-a]pyrimidin-2-yl)(morpholino)methanone(Non-covalent)

6A5.8: 12 residues within 4Å: Chain A: R.89, E.169, E.170, Y.511, W.593, S.594, Y.595, V.620, Y.626, Y.630, N.674, H.704 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.595 Hydrogen bonds: A:R.89, A:E.169, A:E.170, A:Y.626 Water bridges: A:Y.511 pi-Stacking: A:Y.630 pi-Cation interactions: A:R.89 Halogen bonds: A:N.674 6A5.14: 12 residues within 4Å: Chain B: R.89, E.169, E.170, Y.511, W.593, S.594, Y.595, V.620, Y.626, Y.630, N.674, H.704 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.170 Water bridges: B:R.89, B:R.89, B:R.89 pi-Stacking: B:Y.630

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 3 residues within 4Å: Chain A: E.208 Chain B: R.648, T.651 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.651, A:E.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meng, W. et al., Discovery of 6-(Aminomethyl)-5-(2,4-dichlorophenyl)-7-methylimidazo[1,2-a]pyrimidine-2-carboxamides as Potent, Selective Dipeptidyl Peptidase-4 (DPP4) Inhibitors. J.Med.Chem. (2010)

Release Date

2010-08-11

Peptides

Dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2)

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