SMTL ID : 4n8d.1

DPP4 complexed with syn-7aa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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

NAG-NAG-MAN-MAN-MAN.1: 6 residues within 4Å: Chain A: E.29, V.40, N.42, N.47, S.48, S.49 No protein-ligand interaction detected (PLIP)

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

NAG.2: 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.3: 4 residues within 4Å: Chain A: N.181, T.183, Q.270, E.271 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.181, A:T.183, A:E.271, A:E.271 Water bridges: A:N.181, A:T.183 NAG.4: 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 Water bridges: A:T.227, A:K.229 NAG.5: 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.6: 6 residues within 4Å: Chain A: I.281, N.283, M.310, S.311, T.312, R.558 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.312 Hydrogen bonds: A:R.558 Water bridges: A:N.283 NAG.7: 3 residues within 4Å: Chain A: N.482, R.543, D.567 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.543, A:R.543 NAG.12: 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.13: 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:R.109, B:N.112, B:N.112 NAG.14: 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:E.271 Water bridges: B:N.181, B:N.181, B:T.183 NAG.15: 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.16: 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.17: 6 residues within 4Å: Chain B: I.281, N.283, M.310, S.311, T.312, R.558 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.558 Water bridges: B:N.283

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

SO4.8: 4 residues within 4Å: Chain A: R.558, R.559, D.640, N.641 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.558, A:D.640 Salt bridges: A:R.558, A:R.559 SO4.9: 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 SO4.10: 5 residues within 4Å: Chain A: R.620, R.646 Chain B: D.205, E.206, S.207 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.620 Salt bridges: A:R.620, A:R.646 SO4.18: 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:E.108, B:R.109 Water bridges: B:T.106 Salt bridges: B:R.109 SO4.19: 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 SO4.20: 4 residues within 4Å: Chain A: E.206, S.207 Chain B: R.620, R.646 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.620, B:R.646, B:R.646 Salt bridges: B:R.620, B:R.646

2 x 2KS: 1-(cis-1-phenyl-4-{[(2E)-3-phenylprop-2-en-1-yl]oxy}cyclohexyl)methanamine(Non-covalent)

2KS.11: 13 residues within 4Å: Chain A: R.87, E.167, E.168, S.171, F.319, R.320, Y.509, S.592, Y.593, Y.624, Y.628, V.673, H.702 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.319, A:F.319, A:Y.624, A:Y.628, A:V.673 Hydrogen bonds: A:E.168, A:Y.624 pi-Stacking: A:Y.628 pi-Cation interactions: A:R.320 2KS.21: 14 residues within 4Å: Chain B: R.87, E.167, E.168, S.171, F.319, R.320, Y.509, S.592, Y.593, V.618, Y.624, Y.628, V.673, H.702 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.319, B:F.319, B:V.618, B:Y.624, B:Y.628, B:V.673 Hydrogen bonds: B:E.167, B:E.167 pi-Stacking: B:Y.628 pi-Cation interactions: B:R.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Namoto, K. et al., Discovery of C-(1-aryl-cyclohexyl)-methylamines as selective, orally available inhibitors of dipeptidyl peptidase IV. Bioorg.Med.Chem.Lett. (2014)

Release Date

2014-02-12

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4

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