SMTL ID : 2qt9.1

Human dipeptidyl peptidase iv/cd26 in complex with a 4-aryl cyclohexylalanine inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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: 6 residues within 4Å: Chain A: E.67, V.78, N.80, N.85, S.86, S.87 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.78 Hydrogen bonds: A:N.85 Water bridges: A:N.80 NAG-NDG.4: 4 residues within 4Å: Chain A: I.194, N.229, T.231, E.232 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.194 Hydrogen bonds: A:N.229, A:T.231, A:E.232, A:E.232 Water bridges: A:T.265

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: 3 residues within 4Å: Chain A: R.147, P.149, N.150 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain A: N.219, T.221, F.222, N.272, Q.308, E.309, Y.330, E.332 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.222, A:Y.330 Hydrogen bonds: A:N.272, A:E.332, A:E.332 NAG-NAG.5: 7 residues within 4Å: Chain A: I.319, N.321, M.348, S.349, T.350, R.596, D.678 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.596, A:R.596, A:D.678 NAG-NAG.6: 5 residues within 4Å: Chain B: E.67, V.78, N.85, S.86, S.87 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 8 residues within 4Å: Chain B: N.219, T.221, F.222, N.272, Q.308, E.309, Y.330, E.332 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.222, B:Y.330 Water bridges: B:E.332, B:E.332 NAG-NAG.8: 4 residues within 4Å: Chain B: I.194, N.229, T.231, E.232 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.231 NAG-NAG.9: 3 residues within 4Å: Chain B: W.187, T.188, N.281 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.188

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

NAG.10: 4 residues within 4Å: Chain A: E.73, N.74, N.75, N.92 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.73, A:N.74, A:N.75 NAG.11: 3 residues within 4Å: Chain A: W.187, V.279, N.281 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain A: N.520, R.581 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.581, A:R.581, A:R.581 NAG.15: 4 residues within 4Å: Chain B: E.73, N.74, N.75, N.92 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.75 NAG.16: 3 residues within 4Å: Chain B: R.147, I.148, N.150 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.147 Hydrogen bonds: B:R.147 NAG.17: 3 residues within 4Å: Chain B: I.319, N.321, S.349 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.321 Water bridges: B:N.321, B:R.596, B:R.596, B:D.678

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

NA.13: 3 residues within 4Å: Chain A: G.490, L.491, R.492 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.491

2 x 524: (2S,3S)-3-AMINO-4-[(3S)-3-FLUOROPYRROLIDIN-1-YL]-N,N-DIMETHYL-4-OXO-2-(TRANS-4-[1,2,4]TRIAZOLO[1,5-A]PYRIDIN-5-YLCYCLOH EXYL)BUTANAMIDE(Non-covalent)

524.14: 16 residues within 4Å: Chain A: R.125, E.205, E.206, V.207, S.209, F.357, R.358, Y.547, S.630, Y.631, V.656, Y.662, Y.666, N.710, V.711, H.740 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.357, A:F.357, A:F.357, A:R.358, A:V.656, A:V.711 Hydrogen bonds: A:R.125, A:E.205, A:E.205, A:Y.547, A:Y.662, A:N.710 Water bridges: A:R.125, A:S.209, A:S.630 pi-Stacking: A:Y.666 524.18: 16 residues within 4Å: Chain B: R.125, E.205, E.206, V.207, S.209, F.357, R.358, Y.547, S.630, Y.631, V.656, Y.662, Y.666, N.710, V.711, H.740 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.357, B:F.357, B:R.358, B:V.656, B:Y.666, B:V.711 Hydrogen bonds: B:R.125, B:E.205, B:E.205, B:Y.662, B:N.710 Water bridges: B:S.209, B:S.209, B:Y.547, B:S.630, B:S.630 pi-Stacking: B:Y.666 Halogen bonds: B:Y.547

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaelin, D.E. et al., 4-Arylcyclohexylalanine analogs as potent, selective, and orally active inhibitors of dipeptidyl peptidase IV. Bioorg.Med.Chem.Lett. (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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