SMTL ID : 2rgu.1

Crystal structure of complex of human DPP4 and inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 2 residues within 4Å: Chain A: R.109, N.112 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.109 Hydrogen bonds: A:R.109, A:R.109, A:N.112 NAG.2: 6 residues within 4Å: Chain A: E.29, V.40, N.42, N.47, S.48, S.49 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.40 Hydrogen bonds: A:N.47 Water bridges: A:E.29 NAG.3: 3 residues within 4Å: Chain A: W.149, V.241, N.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.243, A:N.243 NAG.4: 5 residues within 4Å: Chain A: T.150, I.156, N.191, T.193, E.194 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.150, A:I.156 Hydrogen bonds: A:N.191, A:E.194 NAG.6: 3 residues within 4Å: Chain B: R.109, I.110, N.112 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.109 Hydrogen bonds: B:R.109, B:N.112, B:N.112 NAG.7: 5 residues within 4Å: Chain B: V.40, N.42, N.47, S.48, S.49 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.40 Hydrogen bonds: B:N.47 Water bridges: B:N.42, B:N.42 NAG.8: 4 residues within 4Å: Chain B: I.156, N.191, T.193, E.194 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.156 Hydrogen bonds: B:N.191, B:T.193, B:E.194, B:E.194 NAG.9: 3 residues within 4Å: Chain B: E.35, N.37, N.54 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.37, B:N.54

2 x 356: 8-[(3R)-3-Aminopiperidin-1-yl]-7-but-2-yn-1-yl-3-methyl-1-[(4-methylquinazolin-2-yl)methyl]-3,7-dihydro-1H-purine-2,6-d ione(Non-covalent)

356.5: 13 residues within 4Å: Chain A: E.167, E.168, F.319, Y.509, W.591, S.592, Y.593, G.594, V.618, Y.624, Y.628, V.673, H.702 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.591, A:W.591, A:Y.593, A:V.618, A:Y.624, A:V.673 Hydrogen bonds: A:E.167, A:E.168, A:Y.593, A:G.594, A:Y.624 Water bridges: A:W.591, A:S.592, A:S.592 pi-Stacking: A:Y.509, A:W.591 356.10: 12 residues within 4Å: Chain B: E.167, E.168, F.319, Y.509, W.591, S.592, Y.593, V.618, Y.624, Y.628, V.673, H.702 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.591, B:W.591, B:W.591, B:Y.593, B:V.618, B:Y.624, B:V.673 Hydrogen bonds: B:Y.593, B:Y.624 Water bridges: B:S.592, B:S.592 pi-Stacking: B:Y.509, B:W.591

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eckhardt, M. et al., 8-(3-(R)-Aminopiperidin-1-yl)-7-but-2-ynyl-3-methyl-1-(4-methyl-quinazolin-2-ylmethyl)-3,7-dihydropurine-2,6-dione (BI 1356), a Highly Potent, Selective, Long-Acting, and Orally Bioavailable DPP-4 Inhibitor for the Treatment of Type 2 Diabetes. J.Med.Chem. (2007)

Release Date

2007-11-06

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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