SMTL ID : 2p8s.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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: 5 residues within 4Å: Chain A: E.29, V.40, N.47, S.48, S.49 No protein-ligand interaction detected (PLIP) 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.184, A:Y.292 Hydrogen bonds: A:N.234, A:E.294 NAG-NAG.4: 4 residues within 4Å: Chain A: I.156, N.191, T.193, E.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.194 NAG-NAG.5: 7 residues within 4Å: Chain A: I.281, N.283, M.310, S.311, T.312, R.558, D.640 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.558, 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:T.183 NAG-NAG.8: 4 residues within 4Å: Chain B: I.156, N.191, T.193, E.194 No protein-ligand interaction detected (PLIP) 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: 2 residues within 4Å: Chain A: 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 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.37, 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: 5 residues within 4Å: Chain B: I.281, N.283, M.310, S.311, T.312 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.558

1 x NA: SODIUM ION(Non-functional Binders)

NA.13: 2 residues within 4Å: Chain A: G.452, L.453 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.453

2 x 417: (1S,2R,5S)-5-[3-(TRIFLUOROMETHYL)-5,6-DIHYDRO[1,2,4]TRIAZOLO[4,3-A]PYRAZIN-7(8H)-YL]-2-(2,4,5-TRIFLUOROPHENYL)CYCLOHEXANAMINE(Non-covalent)

417.14: 14 residues within 4Å: Chain A: R.87, H.88, E.167, E.168, S.171, Y.509, S.592, Y.593, V.618, Y.624, Y.628, N.672, V.673, H.702 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.624, A:V.673 Hydrogen bonds: A:E.167, A:E.168, A:S.171, A:Y.624 pi-Stacking: A:Y.628 Halogen bonds: A:N.672 417.18: 13 residues within 4Å: Chain B: R.87, E.167, E.168, S.171, Y.509, S.592, Y.593, V.618, Y.624, Y.628, N.672, V.673, H.702 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.673 Hydrogen bonds: B:E.167, B:E.168, B:S.171 pi-Stacking: B:Y.628

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biftu, T. et al., Rational design of a novel, potent, and orally bioavailable cyclohexylamine DPP-4 inhibitor by application of molecular modeling and X-ray crystallography of sitagliptin. Bioorg.Med.Chem.Lett. (2007)

Release Date

2007-05-22

Peptides

DIPEPTIDYL PEPTIDASE IV SOLUBLE FORM: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DIPEPTIDYL PEPTIDASE IV SOLUBLE FORM

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