SMTL ID : 3c43.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG.1: 5 residues within 4Å: Chain A: E.29, V.40, N.47, S.48, S.49 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: P.111, N.112 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain A: N.181, T.183, F.184, Q.270, E.271, Y.292, E.294 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.184, A:Y.292 Hydrogen bonds: A:E.294, A:E.294 NAG-NAG.4: 4 residues within 4Å: Chain A: I.156, N.191, T.193, E.194 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain A: I.281, N.283, M.310, S.311, T.312, R.558, D.640 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.558, 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 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.184, B:Y.292 Hydrogen bonds: B:E.294, B:E.294 NAG-NAG.8: 5 residues within 4Å: Chain B: T.150, I.156, N.191, T.193, E.194 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.193 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.35, A:E.35, A:E.35, A:N.36, 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: 3 residues within 4Å: Chain A: L.481, N.482, R.543 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.543, A:R.543, A:R.543 NAG.14: 5 residues within 4Å: Chain B: E.35, N.36, N.37, E.53, N.54 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.53 Hydrogen bonds: B:N.37, B:E.53, B:N.54 NAG.15: 3 residues within 4Å: Chain B: R.109, I.110, N.112 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.109 Hydrogen bonds: B:N.112 Water bridges: B:N.112 NAG.16: 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

2 x 315: (2S,3S)-4-cyclopropyl-3-{(3R,5R)-3-[2-fluoro-4-(methylsulfonyl)phenyl]-1,2,4-oxadiazolidin-5-yl}-1-[(3S)-3-fluoropyrrolidin-1-yl]-1-oxobutan-2-amine(Non-covalent)

315.13: 15 residues within 4Å: Chain A: R.87, E.167, E.168, F.319, Y.509, S.514, Q.515, K.516, S.592, Y.593, V.618, Y.624, Y.628, N.672, V.673 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.618, A:Y.624, A:V.673 Hydrogen bonds: A:R.87, A:E.167, A:E.167, A:Y.509, A:Y.624, A:N.672 Water bridges: A:R.87, A:S.592 pi-Stacking: A:Y.509 315.17: 16 residues within 4Å: Chain B: R.87, E.167, E.168, S.171, F.319, Y.509, S.514, Q.515, K.516, S.592, Y.593, V.618, Y.624, Y.628, N.672, V.673 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.618, B:Y.624, B:V.673 Hydrogen bonds: B:R.87, B:E.167, B:E.167, B:Y.624, B:N.672 Water bridges: B:Y.509, B:S.592 pi-Stacking: B:Y.509 Halogen bonds: B:Y.509

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Edmondson, S.D. et al., Fluoroolefins as amide bond mimics in dipeptidyl peptidase IV inhibitors. Bioorg.Med.Chem.Lett. (2008)

Release Date

2008-04-22

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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