SMTL ID : 3c45.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 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: 6 residues within 4Å: Chain A: E.29, V.40, N.42, 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.184, A:Y.292 Hydrogen bonds: A:E.294, 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 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: 7 residues within 4Å: Chain B: N.181, T.183, F.184, N.234, Q.270, E.271, Y.292 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 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 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: 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.15: 4 residues within 4Å: Chain B: E.35, N.36, N.37, N.54 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.37 NAG.16: 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:R.109, 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 317: (2S,3S)-3-{3-[2-chloro-4-(methylsulfonyl)phenyl]-1,2,4-oxadiazol-5-yl}-1-cyclopentylidene-4-cyclopropyl-1-fluorobutan-2-amine(Non-covalent)

317.14: 18 residues within 4Å: Chain A: R.87, E.167, E.168, S.171, F.319, Y.509, P.512, C.513, 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:Y.628, A:Y.628, A:V.673 Hydrogen bonds: A:E.167, A:E.167, A:Y.509, A:Y.624 Water bridges: A:R.87 pi-Stacking: A:Y.509 Halogen bonds: A:P.512 317.18: 17 residues within 4Å: Chain B: R.87, E.167, E.168, S.171, F.319, Y.509, P.512, C.513, S.514, Q.515, K.516, S.592, V.618, Y.624, Y.628, N.672, V.673 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.618, B:Y.624, B:Y.628, B:Y.628, B:V.673 Hydrogen bonds: B:E.167, B:E.167 Water bridges: B:Y.509 pi-Stacking: B:Y.509 Halogen bonds: B:P.512

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

Related Entries With Identical Sequence