5VTA

Co-Crystal Structure of DPPIV with a Chemibody Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/s41598-018-25848-0
  • Primary Citation of Related Structures:  
    5VTA

  • 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 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., 1120 Veterans Boulevard, South San Francisco, CA, 94080, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4
A, B, C, D
739Rattus norvegicusMutation(s): 0 
Gene Names: Dpp4Cd26
EC: 3.4.14.5
UniProt
Find proteins for P14740 (Rattus norvegicus)
Explore P14740 
Go to UniProtKB:  P14740
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14740
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chainE [auth L],
F [auth E],
I [auth G],
K [auth J]
213Mus musculusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chainG [auth H],
H [auth F],
J [auth I],
L [auth K]
217Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9K4
Query on 9K4

Download Ideal Coordinates CCD File 
EA [auth B],
QA [auth C],
Y [auth A],
YA [auth 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
NAG
Query on NAG

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AA [auth B]
BA [auth B]
CA [auth B]
FA [auth C]
GA [auth C]
AA [auth B],
BA [auth B],
CA [auth B],
FA [auth C],
GA [auth C],
HA [auth C],
IA [auth C],
JA [auth C],
KA [auth C],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
RA [auth D],
SA [auth D],
TA [auth D],
UA [auth D],
VA [auth D],
WA [auth D],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4
Query on PG4

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R [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

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S [auth A],
T [auth A],
XA [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

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DA [auth B]
LA [auth C]
MA [auth C]
NA [auth C]
OA [auth C]
DA [auth B],
LA [auth C],
MA [auth C],
NA [auth C],
OA [auth C],
PA [auth C],
U [auth A],
V [auth A],
W [auth A],
X [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • 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
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary