SMTL ID : 4a5s.1

CRYSTAL STRUCTURE OF HUMAN DPP4 IN COMPLEX WITH A NOVAL HETEROCYCLIC DPP4 INHIBITOR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-MAN-MAN-MAN.1: 5 residues within 4Å: Chain A: E.29, V.40, N.47, S.48, S.49 No protein-ligand interaction detected (PLIP)

2 x N7F: 6-[(3S)-3-AMINOPIPERIDIN-1-YL]-5-BENZYL-4-OXO-3-(QUINOLIN-4-YLMETHYL)-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDINE-7-CARBONITRILE(Non-covalent)

N7F.2: 16 residues within 4Å: Chain A: E.167, E.168, D.507, V.508, Y.509, K.516, W.589, G.590, W.591, S.592, Y.593, V.618, Y.624, Y.628, V.673, H.702 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.593, A:V.618, A:Y.624, A:Y.624, A:V.673 Hydrogen bonds: A:E.168, A:Y.593, A:G.594, A:Y.624 Water bridges: A:R.87 pi-Stacking: A:Y.509, A:W.589, A:Y.628 pi-Cation interactions: A:K.516 N7F.12: 17 residues within 4Å: Chain B: R.87, E.167, E.168, D.507, V.508, Y.509, K.516, W.589, G.590, W.591, S.592, Y.593, V.618, Y.624, Y.628, V.673, H.702 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:W.589, B:W.589, B:W.591, B:Y.593, B:V.618, B:Y.624, B:Y.624, B:V.673 Hydrogen bonds: B:E.167, B:E.168, B:Y.593, B:G.594 Water bridges: B:R.87, B:Y.509, B:K.516 pi-Stacking: B:Y.509, B:Y.628 pi-Cation interactions: B:K.516

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

NAG.3: 3 residues within 4Å: Chain A: R.109, I.110, N.112 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.109 Hydrogen bonds: A:R.109, A:R.109 Water bridges: A:N.112, A:N.112 NAG.4: 4 residues within 4Å: Chain A: N.181, T.183, Q.270, E.271 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.181, A:T.183, A:E.271, A:E.271 Water bridges: A:T.183 NAG.5: 4 residues within 4Å: Chain A: I.156, N.191, T.193, E.194 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.156 Hydrogen bonds: A:N.191, A:E.194, A:E.194 Water bridges: A:T.227 NAG.6: 3 residues within 4Å: Chain A: W.149, V.241, N.243 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.243, A:N.243, A:N.243, A:N.243 NAG.7: 6 residues within 4Å: Chain A: I.281, N.283, M.310, S.311, T.312, R.558 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.558 Water bridges: A:N.283, A:N.283, A:N.283 NAG.8: 4 residues within 4Å: Chain A: L.481, N.482, R.543, D.567 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.543, A:R.543 NAG.16: 6 residues within 4Å: Chain B: E.29, V.40, N.42, N.47, S.48, S.49 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.47 Water bridges: B:E.29, B:N.42 NAG.17: 3 residues within 4Å: Chain B: R.109, I.110, N.112 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.109 Hydrogen bonds: B:R.109, B:R.109 Water bridges: B:Y.80, B:Y.80, B:N.112, B:N.112 NAG.18: 4 residues within 4Å: Chain B: N.181, T.183, Q.270, E.271 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.181, B:E.271 Water bridges: B:T.183, B:D.236 NAG.19: 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:E.194, B:E.194 Water bridges: B:K.229 NAG.20: 3 residues within 4Å: Chain B: W.149, V.241, N.243 4 PLIP interactions: 4 interactions with chain B Water bridges: B:N.243, B:N.243, B:N.243, B:N.243 NAG.21: 6 residues within 4Å: Chain B: I.281, N.283, M.310, S.311, T.312, R.558 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.558, B:R.558 Water bridges: B:N.283

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 4 residues within 4Å: Chain A: R.558, R.559, D.640, N.641 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.558, A:R.559 SO4.10: 4 residues within 4Å: Chain A: T.106, E.107, E.108, R.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.108, A:R.109 Salt bridges: A:R.109 SO4.11: 4 residues within 4Å: Chain A: R.620, R.646 Chain B: E.206, S.207 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.620, A:R.646, A:R.646 Salt bridges: A:R.620, A:R.646 SO4.13: 4 residues within 4Å: Chain B: T.106, E.107, E.108, R.109 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.106, B:E.108, B:R.109 Salt bridges: B:R.109 SO4.14: 4 residues within 4Å: Chain B: R.558, R.559, D.640, N.641 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.640 Salt bridges: B:R.558, B:R.559 SO4.15: 4 residues within 4Å: Chain A: E.206, S.207 Chain B: R.620, R.646 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.620, B:R.646

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sutton, J.M. et al., Novel Heterocyclic Dpp-4 Inhibitors for the Treatment of Type 2 Diabetes. Bioorg.Med.Chem.Lett. (2012)

Release Date

2012-02-08

Peptides

DIPEPTIDYL PEPTIDASE 4 SOLUBLE FORM: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DIPEPTIDYL PEPTIDASE 4 SOLUBLE FORM

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