SMTL ID : 3qbj.1

Crystal structure of dipeptidyl peptidase IV in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-dimer

Ligands

2 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: V.48, N.50, N.55, S.56, S.57 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain B: E.37, V.48, F.49, N.50, N.55, S.56, S.57 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 5 residues within 4Å: Chain A: I.164, N.199, T.201, E.202, K.237 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.202

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

NAG.4: 4 residues within 4Å: Chain A: N.189, T.191, Q.278, E.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.189, A:T.191, A:E.279 NAG.5: 6 residues within 4Å: Chain A: I.289, N.291, M.318, S.319, T.320, R.566 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.318 Hydrogen bonds: A:R.566 NAG.7: 5 residues within 4Å: Chain B: I.164, N.199, T.201, E.202, K.237 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.164 Hydrogen bonds: B:N.199, B:T.201, B:E.202, B:E.202, B:K.237

2 x NXZ: 1-[(3S,4S)-4-amino-1-(6-phenylpyrimidin-4-yl)pyrrolidin-3-yl]piperidin-2-one(Non-covalent)

NXZ.6: 14 residues within 4Å: Chain A: R.95, E.175, E.176, S.179, F.327, R.328, Y.517, S.600, Y.601, Y.632, Y.636, N.680, V.681, H.710 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.327, A:F.327, A:F.327, A:Y.632, A:Y.636, A:V.681 Hydrogen bonds: A:R.95, A:E.175, A:Y.632, A:Y.632, A:N.680 pi-Stacking: A:F.327 NXZ.8: 14 residues within 4Å: Chain B: R.95, E.175, E.176, S.179, F.327, R.328, Y.517, S.600, Y.601, Y.632, Y.636, N.680, V.681, H.710 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.327, B:F.327, B:F.327, B:Y.632, B:Y.636, B:V.681 Hydrogen bonds: B:R.95, B:Y.632, B:Y.632, B:N.680 pi-Stacking: B:F.327

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, S.P., Crystal structure of dipeptidyl peptidase IV in complex with inhibitor. To be Published

Release Date

2012-01-25

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4