SMTL ID : 3opm.1 (2 other biounits)

Crystal Structure of Human DPP4 Bound to TAK-294

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

homo-tetramer

Ligands

4 x LUI: 2-{[3-(aminomethyl)-2-(2-methylpropyl)-1-oxo-4-phenyl-1,2-dihydroisoquinolin-6-yl]oxy}acetamide(Non-covalent)

LUI.1: 13 residues within 4Å: Chain A: R.99, E.179, E.180, S.183, F.331, Y.521, K.528, W.603, S.604, Y.605, Y.636, Y.640, V.685 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.331, A:Y.605, A:Y.636, A:V.685 Hydrogen bonds: A:E.180, A:W.603, A:S.604, A:Y.636 Water bridges: A:W.603 pi-Stacking: A:Y.640 LUI.8: 13 residues within 4Å: Chain B: R.99, E.179, E.180, S.183, F.331, Y.521, K.528, W.603, S.604, Y.605, Y.636, Y.640, V.685 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.331, B:Y.605, B:Y.636, B:Y.640, B:Y.640, B:V.685 Hydrogen bonds: B:E.180, B:W.603 Water bridges: B:K.528, B:W.603, B:S.604 LUI.15: 12 residues within 4Å: Chain C: R.99, E.179, E.180, S.183, F.331, Y.521, K.528, W.603, S.604, Y.636, Y.640, V.685 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.331, C:Y.521, C:Y.636, C:Y.636, C:V.685 Hydrogen bonds: C:E.180, C:K.528, C:W.603, C:Y.636 Water bridges: C:W.603 pi-Stacking: C:Y.640 pi-Cation interactions: C:R.99 LUI.16: 13 residues within 4Å: Chain D: R.99, E.179, E.180, S.183, F.331, Y.521, K.528, W.603, S.604, Y.605, Y.636, Y.640, V.685 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:F.331, D:Y.605, D:Y.636, D:Y.636, D:V.685 Hydrogen bonds: D:E.179, D:E.180, D:K.528, D:W.603 Water bridges: D:W.603, D:S.604 pi-Stacking: D:Y.640

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

NAG.2: 1 residues within 4Å: Chain A: N.124 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain A: N.193, T.195, Q.282, E.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.283 NAG.4: 5 residues within 4Å: Chain A: I.168, N.203, T.205, E.206 Ligands: NAG.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.168 Hydrogen bonds: A:Q.201, A:N.203, A:E.206 NAG.5: 3 residues within 4Å: Chain A: T.205, E.206 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.205 NAG.6: 3 residues within 4Å: Chain A: W.161, V.253, N.255 2 PLIP interactions: 2 interactions with chain D Water bridges: D:K.113, D:Q.115 NAG.7: 6 residues within 4Å: Chain A: I.293, N.295, M.322, S.323, T.324, R.570 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.570 NAG.9: 2 residues within 4Å: Chain B: N.59, S.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.61 NAG.10: 3 residues within 4Å: Chain B: R.121, I.122, N.124 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.121 NAG.11: 4 residues within 4Å: Chain B: I.168, N.203, T.205, E.206 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.168 Hydrogen bonds: B:Q.201, B:E.206, B:E.206 NAG.12: 3 residues within 4Å: Chain B: W.161, V.253, N.255 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.255 NAG.13: 4 residues within 4Å: Chain B: I.293, N.295, Y.296, R.570 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.296 NAG.17: 1 residues within 4Å: Chain D: N.124 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.124, D:N.124 NAG.18: 4 residues within 4Å: Chain D: N.193, T.195, Q.282, E.283 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.193, D:T.195, D:E.283 Water bridges: D:T.195 NAG.19: 6 residues within 4Å: Chain D: I.168, Q.201, N.203, T.205, E.206, K.241 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.168 Hydrogen bonds: D:T.205, D:E.206 NAG.20: 3 residues within 4Å: Chain D: W.161, V.253, N.255 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.255, D:N.255

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

NAG-NAG.14: 5 residues within 4Å: Chain C: I.168, Q.201, N.203, T.205, E.206 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Banno, Y. et al., Identification of 3-aminomethyl-1,2-dihydro-4-phenyl-1-isoquinolones: a new class of potent, selective, and orally active non-peptide dipeptidyl peptidase IV inhibitors that form a unique interaction with Lys554. Bioorg.Med.Chem. (2011)

Release Date

2011-10-19

Peptides

Dipeptidyl peptidase 4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dipeptidyl peptidase 4

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