5VTA | pdb_00005vta

Co-Crystal Structure of DPPIV with a Chemibody Inhibitor

PDB DOI: https://doi.org/10.2210/pdb5VTA/pdb

Classification: HYDROLASE
Organism(s): Rattus norvegicus, Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2017-05-16 Released: 2018-05-09
Deposition Author(s): Wang, Z., Johnstone, S., Cheng, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.300 (Depositor), 0.300 (DCC)
R-Value Work:
0.250 (Depositor), 0.253 (DCC)
R-Value Observed:
0.252 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 29765112 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-018-25848-0
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 535.92 kDa
Atom Count: 33,875
Modeled Residue Count: 4,161
Deposited Residue Count: 4,676
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A, B, C, D	739	Rattus norvegicus	Mutation(s): 0 Gene Names: Dpp4, Cd26 EC: 3.4.14.5
UniProt
Find proteins for P14740 (Rattus norvegicus) Explore P14740 Go to UniProtKB: P14740
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14740
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P14740-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	E [auth L], F [auth E], I [auth G], K [auth J]	213	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	G [auth H], H [auth F], J [auth I], L [auth K]	217	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9K4 Query on 9K4 Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain QA [auth C] SDF format, chain Y [auth A] SDF format, chain YA [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain QA [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth D]	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		Interactions Focus chain EA [auth B] Focus chain QA [auth C] Focus chain Y [auth A] Focus chain YA [auth D] Interactions & Density Focus chain EA [auth B] Focus chain QA [auth C] Focus chain Y [auth A] Focus chain YA [auth D]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain Z [auth B] SDF format, chain SA [auth D] SDF format, chain RA [auth D] SDF format, chain Q [auth A] SDF format, chain IA [auth C] SDF format, chain FA [auth C] SDF format, chain CA [auth B] SDF format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain TA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain AA [auth B]	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		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain Z [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain XA [auth D] SDF format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain XA [auth D] MOL2 format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain XA [auth D] mmCIF format, chain T [auth A]	S [auth A], T [auth A], XA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Focus chain T [auth A] Focus chain XA [auth D] Interactions & Density Focus chain S [auth A] Focus chain T [auth A] Focus chain XA [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain PA [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain PA [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain PA [auth C]	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		Interactions Focus chain DA [auth B] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain DA [auth B] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.300 (Depositor), 0.300 (DCC)
R-Value Work: 0.250 (Depositor), 0.253 (DCC)
R-Value Observed: 0.252 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.325	α = 62.34
b = 123.229	β = 77.21
c = 129.018	γ = 75.91

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-05-09

Deposition Author(s):

Wang, Z.

Johnstone, S.

Cheng, A.

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
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Structure summary