SMTL ID : 4n8e.1

DPP4 complexed with compound 12a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.109 Hydrogen bonds: A:R.109, A:R.109 Water bridges: 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:T.183, A:T.183 NAG.4: 5 residues within 4Å: Chain A: I.156, N.191, T.193, E.194, K.229 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.156 Hydrogen bonds: A:N.191, A:T.193, A:E.194, A:K.229 Water bridges: A:E.194, A:T.227 NAG.5: 3 residues within 4Å: Chain A: W.149, V.241, N.243 2 PLIP interactions: 2 interactions with chain A Water bridges: 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.312 Hydrogen bonds: A:N.283, A:N.283 Water bridges: A:R.558 NAG.7: 3 residues within 4Å: Chain A: N.482, F.486, R.543 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.486 Hydrogen bonds: A:R.543, A:R.543, A:R.543 NAG.12: 5 residues within 4Å: Chain B: V.40, N.42, N.47, S.48, S.49 No protein-ligand interaction detected (PLIP) NAG.13: 2 residues within 4Å: Chain B: R.109, N.112 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.109, B:R.109 NAG.14: 4 residues within 4Å: Chain B: N.181, T.183, Q.270, E.271 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.181, B:E.271 NAG.15: 5 residues within 4Å: Chain B: I.156, N.191, T.193, E.194, K.229 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.156 Hydrogen bonds: B:N.191, B:E.194, B:E.194, B:K.229 NAG.16: 3 residues within 4Å: Chain B: W.149, V.241, N.243 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.243 Water bridges: B:N.243 NAG.17: 5 residues within 4Å: Chain B: I.281, N.283, M.310, S.311, R.558 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.558 Water bridges: B:N.283, 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.559, 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.108, A:R.109 Water bridges: A:R.109 Salt bridges: A:R.109 SO4.10: 3 residues within 4Å: Chain A: R.620, R.646 Chain B: S.207 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.620, A:R.646 SO4.18: 4 residues within 4Å: Chain B: T.106, E.107, E.108, R.109 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.106, B:E.108, B:R.109 Water bridges: B:E.108 Salt bridges: B:R.109 SO4.19: 4 residues within 4Å: Chain B: R.558, R.559, D.640, N.641 2 PLIP interactions: 2 interactions with chain B 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 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Water bridges: B:R.620, B:R.620, A:S.207, A:S.207 Salt bridges: B:R.620, B:R.646

2 x 2KV: 1-[cis-4-(aminomethyl)-4-(3-chlorophenyl)cyclohexyl]piperidin-2-one(Non-covalent)

2KV.11: 14 residues within 4Å: Chain A: R.87, E.167, E.168, S.171, F.319, Y.509, S.592, Y.593, V.618, W.621, Y.624, Y.628, V.673, H.702 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.319, A:F.319, A:Y.628, A:V.673 Hydrogen bonds: A:E.168, A:Y.624 pi-Stacking: A:Y.628 2KV.21: 14 residues within 4Å: Chain B: R.87, E.167, E.168, S.171, F.319, Y.509, S.592, Y.593, V.618, W.621, Y.624, Y.628, V.673, H.702 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.319, B:F.319, B:Y.628, B:V.673 Hydrogen bonds: B:E.167, B:E.168 pi-Stacking: B:Y.628

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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