SMTL ID : 3sx4.1

Crystal structure of human dpp-iv in complex with sa-(+)-3-(aminomethyl)-4-(2,4-dichlorophenyl)-6-(2-methoxyphenyl)- 2-methyl-5h-pyrrolo[3,4-b]pyridin-7(6h)-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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: T.152, I.158, N.193, T.195, E.196, K.231 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: I.158, N.193, T.195, E.196 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.195

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

NAG.3: 4 residues within 4Å: Chain A: V.42, N.49, S.50, S.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.49 NAG.4: 3 residues within 4Å: Chain A: I.112, P.113, N.114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.114 NAG.5: 6 residues within 4Å: Chain A: N.183, T.185, D.238, Q.272, E.273, Y.294 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.185, A:T.185, A:E.273 NAG.6: 3 residues within 4Å: Chain A: W.151, V.243, 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, F.488, R.545, D.569 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.483, A:F.488 Hydrogen bonds: A:N.484, A:R.545, A:R.545 NAG.9: 6 residues within 4Å: Chain B: V.42, F.43, N.44, N.49, S.50, S.51 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.49 NAG.10: 3 residues within 4Å: Chain B: E.37, N.39, N.56 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.37, B:N.39, B:N.56 NAG.11: 5 residues within 4Å: Chain B: H.64, N.83, R.111, I.112, N.114 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.111 Hydrogen bonds: B:H.64, B:N.83, B:N.114 NAG.12: 4 residues within 4Å: Chain B: N.183, T.185, Q.272, E.273 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.185, B:E.273 NAG.13: 2 residues within 4Å: Chain B: W.151, N.245 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.245 NAG.14: 5 residues within 4Å: Chain B: L.483, N.484, R.545, E.568, D.569 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.483 Hydrogen bonds: B:R.545, B:E.568

2 x KXA: 3-(aminomethyl)-4-(2,4-dichlorophenyl)-6-(2-methoxyphenyl)-2-methyl-5,6-dihydro-7H-pyrrolo[3,4-b]pyridin-7-one(Non-covalent)

KXA.8: 12 residues within 4Å: Chain A: R.89, E.169, E.170, Y.511, S.594, Y.595, V.620, W.623, Y.626, Y.630, N.674, H.704 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.511, A:Y.595 Hydrogen bonds: A:R.89, A:E.169, A:E.170, A:Y.626 pi-Stacking: A:Y.630 Halogen bonds: A:N.674 KXA.15: 13 residues within 4Å: Chain B: R.89, E.169, E.170, Y.511, W.593, S.594, Y.595, V.620, W.623, Y.626, Y.630, N.674, H.704 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.511, B:W.593, B:Y.626 Hydrogen bonds: B:R.89, B:E.170 pi-Stacking: B:Y.630 Halogen bonds: B:N.674

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., 7-Oxopyrrolopyridine-derived DPP4 inhibitors-mitigation of CYP and hERG liabilities via introduction of polar functionalities in the active site. Bioorg.Med.Chem.Lett. (2011)

Release Date

2011-10-26

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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