SMTL ID : 2oph.1

Human dipeptidyl peptidase IV in complex with an alpha amino acid inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

NAG-NDG.1: 5 residues within 4Å: Chain A: E.29, V.40, N.47, S.48, S.49 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.40 Hydrogen bonds: A:N.47 Water bridges: A:N.42, A:N.42, A:S.49, A:S.49 NAG-NDG.4: 5 residues within 4Å: Chain A: I.156, N.191, T.193, E.194, K.229 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.156 Hydrogen bonds: A:N.191, A:T.193, A:E.194

7 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.109, I.110, P.111, N.112 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain A: N.181, T.183, F.184, N.234, Q.270, E.271, Y.292, E.294 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.184, A:Y.292 Hydrogen bonds: A:N.234, A:E.294, A:E.294, A:E.294 NAG-NAG.5: 6 residues within 4Å: Chain A: I.281, N.283, M.310, S.311, T.312, R.558 2 PLIP interactions: 2 interactions with chain A Water bridges: 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 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.184, B:Y.292 Water bridges: 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: 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: 2 residues within 4Å: Chain A: N.482, R.543 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: 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 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.109 Hydrogen bonds: B:R.109, B:N.112 Water bridges: B:N.112 NAG.17: 6 residues within 4Å: Chain B: I.281, N.283, M.310, S.311, T.312, R.558 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.283

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 277: N-(TRANS-4-{(1S,2S)-2-AMINO-3-[(3S)-3-FLUOROPYRROLIDIN-1-YL]-1-METHYL-3-OXOPROPYL}CYCLOHEXYL)-N-METHYLACETAMIDE(Non-covalent)

277.14: 14 residues within 4Å: Chain A: R.87, E.167, E.168, S.171, F.319, R.320, Y.509, 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:F.319, A:F.319, A:V.618, A:Y.624, A:V.673 Hydrogen bonds: A:R.87, A:E.167, A:E.167, A:R.320, A:Y.624, A:N.672 Water bridges: A:S.592 277.18: 14 residues within 4Å: Chain B: R.87, E.167, E.168, S.171, F.319, R.320, Y.509, S.592, Y.593, V.618, Y.624, Y.628, N.672, V.673 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.319, B:F.319, B:V.618, B:Y.624, B:V.673 Hydrogen bonds: B:R.87, B:E.167, B:E.167, B:R.320, B:R.320, B:Y.624, B:N.672 Water bridges: B:S.171, B:S.592

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duffy, J.L. et al., 4-Aminophenylalanine and 4-aminocyclohexylalanine derivatives as potent, selective, and orally bioavailable inhibitors of dipeptidyl peptidase IV. Bioorg.Med.Chem.Lett. (2007)

Release Date

2007-05-08

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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