SMTL ID : 5vta.3 (3 other biounits)

Co-Crystal Structure of DPPIV with a Chemibody Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: E.29, L.40, H.45, N.47, S.49 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.40 NAG.2: 6 residues within 4Å: Chain A: E.35, N.36, N.37, N.54, E.58 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.37, A:N.54 NAG.3: 2 residues within 4Å: Chain A: N.112, N.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.113 NAG.4: 5 residues within 4Å: Chain A: I.156, Q.189, 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.5: 2 residues within 4Å: Chain A: I.281, N.283 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain A: N.485, R.546, D.570 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.485

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 5 residues within 4Å: Chain A: N.54, E.58 Chain C: D.31, Y.32 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.58 EDO.8: 5 residues within 4Å: Chain A: D.66, E.79, Y.82, Y.90 Ligands: 9K4.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.66 EDO.9: 2 residues within 4Å: Chain A: R.87, S.595 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.87, A:R.87, A:S.595, A:S.595 EDO.10: 4 residues within 4Å: Chain A: D.66, E.79, W.116, I.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.79 EDO.11: 6 residues within 4Å: Chain A: F.349, R.353, K.354, Q.357, V.358, C.359 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.353, A:Q.357

1 x 9K4: 2-{4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]piperazin-1-yl}-N-(22-oxo-3,6,9,12,15,18-hexaoxa-21-azatricosan-1-yl)acetamide(Non-covalent)

9K4.12: 15 residues within 4Å: Chain A: Y.82, R.87, E.167, E.168, F.319, Y.512, S.595, Y.596, V.621, Y.627, Y.631, N.675, V.676, H.705 Ligands: EDO.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.631, A:V.676 Hydrogen bonds: A:R.87, A:E.167, A:Y.627, A:N.675 pi-Stacking: A:Y.627 Halogen bonds: A:N.675

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, A.C. et al., Structure-guided Discovery of Dual-recognition Chemibodies. Sci Rep (2018)

Release Date

2018-05-09

Peptides

Dipeptidyl peptidase 4: A
Fab light chain: B
Fab heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

C
F

Dipeptidyl peptidase 4

Fab light chain

Fab heavy chain

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