SMTL ID : 2rip.1

Structure of DPPIV in complex with an inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.1: 6 residues within 4Å: Chain A: V.41, F.42, N.43, N.48, S.49, S.50 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.8: 6 residues within 4Å: Chain B: V.41, F.42, N.43, N.48, S.49, S.50 No protein-ligand interaction detected (PLIP)

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.2: 4 residues within 4Å: Chain A: R.110, I.111, P.112, N.113 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: R.110, I.111, P.112, N.113 No protein-ligand interaction detected (PLIP)

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

NAG.3: 4 residues within 4Å: Chain A: N.182, T.184, Q.271, E.272 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.184, A:T.184, A:E.272, A:E.272 NAG.4: 2 residues within 4Å: Chain A: I.157, N.192 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.157 Hydrogen bonds: A:N.192 NAG.5: 3 residues within 4Å: Chain A: W.150, V.242, N.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.244 NAG.6: 3 residues within 4Å: Chain A: I.282, N.284, S.312 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain B: N.182, T.184, Q.271, E.272 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.184, B:T.184, B:E.272 NAG.11: 2 residues within 4Å: Chain B: I.157, N.192 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.157 Hydrogen bonds: B:N.192 NAG.12: 3 residues within 4Å: Chain B: W.150, V.242, N.244 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.244 NAG.13: 3 residues within 4Å: Chain B: I.282, N.284, S.312 No protein-ligand interaction detected (PLIP)

2 x 34Q: (3R,4R)-4-(pyrrolidin-1-ylcarbonyl)-1-(quinoxalin-2-ylcarbonyl)pyrrolidin-3-amine(Non-covalent)

34Q.7: 13 residues within 4Å: Chain A: R.88, E.168, E.169, S.172, F.320, R.321, Y.510, S.593, V.619, Y.625, Y.629, N.673, V.674 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.320, A:R.321, A:V.619, A:Y.625, A:V.674 Hydrogen bonds: A:R.88, A:E.168, A:S.593, A:Y.625, A:Y.625, A:N.673 34Q.14: 13 residues within 4Å: Chain B: R.88, E.168, E.169, S.172, F.320, R.321, Y.510, S.593, V.619, Y.625, Y.629, N.673, V.674 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.320, B:R.321, B:V.619, B:Y.625, B:V.674 Hydrogen bonds: B:R.88, B:S.593, B:Y.625, B:Y.625, B:N.673

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Corbett, J.W. et al., Design and synthesis of potent amido- and benzyl-substituted cis-3-amino-4-(2-cyanopyrrolidide)pyrrolidinyl DPP-IV inhibitors. Bioorg.Med.Chem.Lett. (2007)

Release Date

2008-03-18

Peptides

Dipeptidyl peptidase 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dipeptidyl peptidase 4