SMTL ID : 5vta.2 (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

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

NAG.1: 1 residues within 4Å: Chain A: N.47 No protein-ligand interaction detected (PLIP) NAG.2: 5 residues within 4Å: Chain A: E.35, N.36, N.37, N.54, E.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.35, A:N.37, A:N.54 NAG.3: 4 residues within 4Å: Chain A: I.156, N.191, T.193, K.229 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.156 NAG.4: 3 residues within 4Å: Chain A: N.485, R.546, D.570 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.485, A:R.546

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

EDO.5: 7 residues within 4Å: Chain A: A.513, S.517, F.543, D.544, G.545, S.548, Q.571 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.513, A:G.545, A:Q.571

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)

9K4.6: 18 residues within 4Å: Chain A: D.62, S.65, Y.82, R.87, E.167, E.168, F.319, Y.512, S.595, Y.596, V.621, W.624, Y.627, Y.631, N.675, V.676, H.705 Chain B: C.30 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.676 Hydrogen bonds: A:E.167, A:E.168 pi-Stacking: A:Y.627, A:Y.631

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
B

B
G

C
I

Dipeptidyl peptidase 4

Fab light chain

Fab heavy chain

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