SMTL ID : 2buc.2 (1 other biounit)

Crystal Structure Of Porcine Dipeptidyl Peptidase IV (CD26) in Complex with a Tetrahydroisoquinoline Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

5 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: 9 residues within 4Å: Chain A: R.559, G.561, T.562, E.566, M.600, Y.644, N.647, S.648, R.653 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.559, A:E.566 NAG-NAG.2: 4 residues within 4Å: Chain B: E.35, N.36, N.37, N.54 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain B: T.150, I.156, Q.189, N.191, T.193, E.194, K.229 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain B: A.281, N.283, S.311, T.312, R.558, E.639, D.640 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.558, B:E.639 NAG-NAG.5: 9 residues within 4Å: Chain B: R.559, G.561, T.562, E.566, M.600, Y.644, N.647, S.648, R.653 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.559

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

NAG.6: 3 residues within 4Å: Chain A: N.42, N.47, S.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.42, A:N.47 NAG.7: 2 residues within 4Å: Chain A: N.37, N.54 No protein-ligand interaction detected (PLIP) NAG.8: 7 residues within 4Å: Chain A: T.150, I.156, Q.189, N.191, T.193, E.194, K.229 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.150, A:I.156 Hydrogen bonds: A:N.191, A:T.193, A:E.194 Water bridges: A:Q.189, A:K.229 NAG.9: 1 residues within 4Å: Chain A: N.241 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.241 NAG.10: 3 residues within 4Å: Chain A: A.281, N.283, D.640 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.640 Water bridges: A:N.283, A:N.283, A:R.558 NAG.14: 4 residues within 4Å: Chain B: N.42, Y.45, N.47, S.49 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.47, B:S.49 NAG.15: 1 residues within 4Å: Chain B: N.241 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.241, B:N.241, B:N.241

2 x 008: (S)-2-[(R)-3-AMINO-4-(2-FLUORO-PHENYL)-BUTYRYL]-1,2,3,4-TETRAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID AMIDE(Non-covalent)

008.11: 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, Y.624, Y.628, N.672, V.673, H.702 Ligands: SO4.13 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.319, A:F.319, A:R.320, A:Y.593, A:V.618, A:Y.624, A:V.673 Hydrogen bonds: A:E.167, A:E.168, A:Y.624 pi-Stacking: A:Y.628 008.16: 16 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, Y.624, Y.628, N.672, V.673, H.702 Ligands: SO4.18 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.319, B:F.319, B:Y.593, B:Y.624, B:V.673 Hydrogen bonds: B:E.167, B:E.168, B:Y.624 pi-Stacking: B:Y.628

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.12: 6 residues within 4Å: Chain A: A.322, E.323, H.325, I.336, G.368, I.369 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.323, A:E.323, A:I.369 Salt bridges: A:H.325 SO4.13: 5 residues within 4Å: Chain A: R.87, Y.509, S.592, H.702 Ligands: 008.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.509, A:S.592 Salt bridges: A:R.87, A:H.702 SO4.17: 7 residues within 4Å: Chain B: A.322, E.323, H.325, I.336, I.367, G.368, I.369 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.323, B:I.369 Water bridges: B:E.323 Salt bridges: B:H.325 SO4.18: 5 residues within 4Å: Chain B: R.87, Y.509, S.592, H.702 Ligands: 008.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.592 Salt bridges: B:R.87, B:H.702

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nordhoff, S. et al., The reversed binding of beta-phenethylamine inhibitors of DPP-IV: X-ray structures and properties of novel fragment and elaborated inhibitors. Bioorg. Med. Chem. Lett. (2006)

Release Date

2006-01-23

Peptides

DIPEPTIDYL PEPTIDASE IV: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

DIPEPTIDYL PEPTIDASE IV

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