2QOE

Human Dipeptidyl Peptidase IV in complex with a Triazolopiperazine-based beta amino acid Inhibitor

PDB DOI: https://doi.org/10.2210/pdb2QOE/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2007-07-20 Released: 2007-11-06
Deposition Author(s): Scapin, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.212
R-Value Work: 0.170
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Design, synthesis, and biological evaluation of triazolopiperazine-based beta-amino amides as potent, orally active dipeptidyl peptidase IV (DPP-4) inhibitors.

Kowalchick, J.E., Leiting, B., Pryor, K.D., Marsilio, F., Wu, J.K., He, H., Lyons, K.A., Eiermann, G.J., Petrov, A., Scapin, G., Patel, R.A., Thornberry, N.A., Weber, A.E., Kim, D.

(2007) Bioorg Med Chem Lett 17: 5934-5939

PubMed: 17827003 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2007.07.100
Primary Citation of Related Structures:
2QOE

PubMed Abstract:
Various beta-amino amides containing triazolopiperazine heterocycles have been prepared and evaluated as potent, selective, orally active dipeptidyl peptidase IV (DPP-4) inhibitors. These compounds display excellent oral bioavailability and good overall pharmacokinetic profiles in preclinical species. Moreover, in vivo efficacy in an oral glucose tolerance test in lean mice is demonstrated.

Organizational Affiliation

Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 2000, Rahway, NJ 07065, USA. jennifer_kowalchick@yahoo.com

Macromolecule Content

Total Structure Weight: 174.52 kDa
Atom Count: 13,312
Modelled Residue Count: 1,456
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A, B	728	Homo sapiens	Mutation(s): 1 Gene Names: DPP4, ADCP2, CD26 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens) Explore P27487 Go to UniProtKB: P27487
PHAROS: P27487 GTEx: ENSG00000197635
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27487
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P27487-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth S], F [auth E]	2		N-Glycosylation	Interactions Focus chain C [auth S] Focus chain F [auth E] Interactions & Density Focus chain C [auth S] Focus chain F [auth E]
Glycosylation Resources
GlyTouCan: G07375KG GlyCosmos: G07375KG GlyGen: G07375KG

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C], E [auth D], G [auth F], H [auth G], I [auth H], D [auth C], E [auth D], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J]	2		N-Glycosylation	Interactions Focus chain D [auth C] Focus chain E [auth D] Focus chain G [auth F] Focus chain H [auth G] Focus chain I [auth H] Focus chain J [auth I] Focus chain K [auth J] Interactions & Density Focus chain D [auth C] Focus chain E [auth D] Focus chain G [auth F] Focus chain H [auth G] Focus chain I [auth H] Focus chain J [auth I] Focus chain K [auth J]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
448 Query on 448 Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain R [auth B] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] mmCIF format, chain N [auth A] mmCIF format, chain R [auth B]	N [auth A], R [auth B]	(2R)-4-[(8R)-8-METHYL-2-(TRIFLUOROMETHYL)-5,6-DIHYDRO[1,2,4]TRIAZOLO[1,5-A]PYRAZIN-7(8H)-YL]-4-OXO-1-(2,4,5-TRIFLUOROPHENYL)BUTAN-2-AMINE C₁₇ H₁₇ F₆ N₅ O FDEXEPZGMKFCTG-PSASIEDQSA-N		Interactions Focus chain N [auth A] Focus chain R [auth B] Interactions & Density Focus chain N [auth A] Focus chain R [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	L [auth A], O [auth B], P [auth B], Q [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
448	PDBBind: 2QOE	IC50: 25 (nM) from 1 assay(s)
448	BindingDB: 2QOE	IC50: 25 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.212
R-Value Work: 0.170
R-Value Observed: 0.172
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.126	α = 90
b = 125.296	β = 90
c = 136.832	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-11-06

Deposition Author(s):

Scapin, G.

Revision History (Full details and data files)

Version 1.0: 2007-11-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2021-10-20
Changes: Database references, Structure summary
Version 2.2: 2024-10-09
Changes: Data collection, Structure summary