SMTL ID : 3d4l.1

Human dipeptidyl peptidase IV/CD26 in complex with a novel inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

NAG-NDG.1: 5 residues within 4Å: Chain A: E.29, V.40, N.47, S.48, S.49 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.40 Hydrogen bonds: A:N.47 Water bridges: A:E.29, A:N.42 NAG-NDG.4: 5 residues within 4Å: Chain A: I.156, N.191, T.193, E.194, K.229 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.156 Hydrogen bonds: A:N.191, A:T.193, A:E.194 Water bridges: A:K.229

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

NAG-NAG.2: 2 residues within 4Å: Chain A: P.111, N.112 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain A: N.181, T.183, F.184, N.234, Q.270, E.271, Y.292, E.294 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.184, A:Y.292 Hydrogen bonds: A:N.234, A:E.294, A:E.294 NAG-NAG.5: 7 residues within 4Å: Chain A: I.281, N.283, M.310, S.311, T.312, R.558, D.640 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.640 NAG-NAG.6: 5 residues within 4Å: Chain B: E.29, V.40, N.47, S.48, S.49 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 8 residues within 4Å: Chain B: N.181, T.183, F.184, N.234, Q.270, E.271, Y.292, E.294 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.184, B:Y.292 NAG-NAG.8: 4 residues within 4Å: Chain B: I.156, N.191, T.193, E.194 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: W.149, T.150, N.243 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.150

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

NAG.10: 4 residues within 4Å: Chain A: E.35, N.36, N.37, N.54 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.36, A:N.37, A:N.37 NAG.11: 3 residues within 4Å: Chain A: W.149, V.241, N.243 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain A: N.482, R.543 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.543, A:R.543 NAG.15: 4 residues within 4Å: Chain B: E.35, N.36, N.37, N.54 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.37, B:N.37 NAG.16: 3 residues within 4Å: Chain B: R.109, I.110, N.112 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.109 Hydrogen bonds: B:N.112 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:N.283, B:R.558

1 x NA: SODIUM ION(Non-functional Binders)

NA.13: 3 residues within 4Å: Chain A: G.452, L.453, R.454 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.453

2 x 605: 4'-[(1R)-1-amino-2-(2,5-difluorophenyl)ethyl]biphenyl-3-carboxamide(Non-covalent)

605.14: 17 residues within 4Å: Chain A: R.87, E.167, E.168, V.169, S.171, F.319, R.320, Y.509, S.592, Y.593, V.618, W.621, Y.624, Y.628, N.672, V.673, H.702 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.319, A:F.319, A:V.618, A:Y.624, A:Y.628, A:V.673 Hydrogen bonds: A:E.167, A:E.168, A:S.171, A:R.320, A:Y.624 Water bridges: A:R.320 pi-Stacking: A:F.319, A:Y.628 605.18: 17 residues within 4Å: Chain B: R.87, E.167, E.168, V.169, S.171, F.319, R.320, Y.509, S.592, Y.593, V.618, W.621, Y.624, Y.628, N.672, V.673, H.702 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.319, B:F.319, 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.168, B:S.171, B:R.320 Water bridges: B:R.320 pi-Stacking: B:Y.628

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liang, G.B. et al., Discovery of new binding elements in DPP-4 inhibition and their applications in novel DPP-4 inhibitor design. Bioorg.Med.Chem.Lett. (2008)

Release Date

2008-07-01

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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