SMTL ID : 1rwq.1

Human Dipeptidyl peptidase IV in complex with 5-aminomethyl-6-(2,4-dichloro-phenyl)-2-(3,5-dimethoxy-phenyl)-pyrimidin-4-ylamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: R.109, I.110, P.111, N.112 No protein-ligand interaction detected (PLIP) NAG.2: 4 residues within 4Å: Chain A: V.40, N.47, S.48, S.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.47 NAG.3: 2 residues within 4Å: Chain A: W.149, N.243 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.243 NAG.4: 4 residues within 4Å: Chain A: I.156, N.191, T.193, K.229 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.156 Hydrogen bonds: A:N.191, A:K.229 NAG.6: 2 residues within 4Å: Chain B: N.81, N.112 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.81, B:N.112 NAG.7: 6 residues within 4Å: Chain B: V.40, F.41, N.42, N.47, S.48, S.49 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.40 Hydrogen bonds: B:N.47, B:S.49 NAG.8: 4 residues within 4Å: Chain B: I.156, N.191, T.193, E.194 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.156 Hydrogen bonds: B:N.191, B:T.193, B:E.194, B:E.194 NAG.9: 3 residues within 4Å: Chain B: E.35, N.37, N.54 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.37, B:N.54

2 x 5AP: 5-(AMINOMETHYL)-6-(2,4-DICHLOROPHENYL)-2-(3,5-DIMETHOXYPHENYL)PYRIMIDIN-4-AMINE(Non-covalent)

5AP.5: 12 residues within 4Å: Chain A: R.87, E.167, E.168, Y.509, S.592, Y.593, V.618, W.621, Y.624, Y.628, N.672, H.702 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.624 Hydrogen bonds: A:R.87, A:E.167, A:E.167, A:E.168, A:Y.624, A:N.672 Water bridges: A:Y.509 pi-Stacking: A:Y.628 Halogen bonds: A:N.672 5AP.10: 12 residues within 4Å: Chain B: R.87, E.167, E.168, Y.509, S.592, Y.593, V.618, W.621, Y.624, Y.628, N.672, H.702 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.624 Hydrogen bonds: B:R.87, B:E.167, B:E.168, B:Y.509 Water bridges: B:R.87 pi-Stacking: B:Y.628 Halogen bonds: B:N.672

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peters, J.U. et al., Aminomethylpyrimidines as novel DPP-IV inhibitors: a 10(5)-fold activity increase by optimization of aromatic substituents. Bioorg.Med.Chem.Lett. (2004)

Release Date

2004-12-17

Peptides

Dipeptidyl peptidase IV: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase IV

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