5VTA

Co-Crystal Structure of DPPIV with a Chemibody Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-guided Discovery of Dual-recognition Chemibodies.

Cheng, A.C.Doherty, E.M.Johnstone, S.DiMauro, E.F.Dao, J.Luthra, A.Ye, J.Tang, J.Nixey, T.Min, X.Tagari, P.Miranda, L.P.Wang, Z.

(2018) Sci Rep 8: 7570-7570

  • DOI: 10.1038/s41598-018-25848-0

  • PubMed Abstract: 
  • Small molecules and antibodies each have advantages and limitations as therapeutics. Here, we present for the first time to our knowledge, the structure-guided design of "chemibodies" as small molecule-antibody hybrids that offer dual recognition of ...

    Small molecules and antibodies each have advantages and limitations as therapeutics. Here, we present for the first time to our knowledge, the structure-guided design of "chemibodies" as small molecule-antibody hybrids that offer dual recognition of a single target by both a small molecule and an antibody, using DPP-IV enzyme as a proof of concept study. Biochemical characterization demonstrates that the chemibodies present superior DPP-IV inhibition compared to either small molecule or antibody component alone. We validated our design by successfully solving a co-crystal structure of a chemibody in complex with DPP-IV, confirming specific binding of the small molecule portion at the interior catalytic site and the Fab portion at the protein surface. The discovery of chemibodies presents considerable potential for novel therapeutics that harness the power of both small molecule and antibody modalities to achieve superior specificity, potency, and pharmacokinetic properties.


    Organizational Affiliation

    Department of Therapeutic Discovery, Amgen Discovery Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA, 91320, USA.,Department of Therapeutic Discovery, Amgen Discovery Research, Amgen Inc., 1120 Veterans Boulevard, South San Francisco, CA, 94080, USA.,Department of Therapeutic Discovery, Amgen Discovery Research, Amgen Inc., 1120 Veterans Boulevard, South San Francisco, CA, 94080, USA. zwang@amgen.com.,Department of Therapeutic Discovery, Amgen Discovery Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA, 91320, USA. lesm@amgen.com.,Department of Therapeutic Discovery, Amgen Discovery Research, Amgen Inc., 360 Binney Street, Cambridge, MA, 02142, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 4
A, B, C, D
739Rattus norvegicusMutation(s): 0 
Gene Names: Dpp4 (Cd26)
EC: 3.4.14.5
Find proteins for P14740 (Rattus norvegicus)
Go to UniProtKB:  P14740
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab light chain
L, E, G, J
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab heavy chain
H, F, I, K
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9K4
Query on 9K4

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Download CCD File 
A, B, C, D
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
C32 H52 F3 N5 O9
UFCDLSMAWGWQEO-HHHXNRCGSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A, D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.250 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 120.325α = 62.34
b = 123.229β = 77.21
c = 129.018γ = 75.91
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-05-30
    Type: Data collection, Database references