2HHA

The structure of DPP4 in complex with an oxadiazole inhibitor

PDB DOI: https://doi.org/10.2210/pdb2HHA/pdb

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

Deposited: 2006-06-28 Released: 2006-09-19
Deposition Author(s): Scapin, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.233
R-Value Work: 0.185
R-Value Observed: 0.206

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of potent, selective, and orally bioavailable oxadiazole-based dipeptidyl peptidase IV inhibitors.

Xu, J., Wei, L., Mathvink, R.J., Edmondson, S.D., Eiermann, G.J., He, H., Leone, J.F., Leiting, B., Lyons, K.A., Marsilio, F., Patel, R.A., Patel, S.B., Petrov, A., Scapin, G., Wu, J.K., Thornberry, N.A., Weber, A.E.

(2006) Bioorg Med Chem Lett 16: 5373-5377

PubMed: 16919457 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2006.07.061
Primary Citation of Related Structures:
2HHA

PubMed Abstract:
A novel series of oxadiazole based amides have been shown to be potent DPP-4 inhibitors. The optimized compound 43 exhibited excellent selectivity over a variety of DPP-4 homologs.

Organizational Affiliation

Department of Medicinal Chemistry, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA. Jinyou_Xu@merck.com

Macromolecule Content

Total Structure Weight: 174.88 kDa
Atom Count: 13,209
Modelled Residue Count: 1,456
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein DPP4	A, B	728	Homo sapiens	Mutation(s): 1 Gene Names: DPP4 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens) Explore P27487 Go to UniProtKB: P27487
GTEx: ENSG00000197635
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27487
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P27487-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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, F	2		N-Glycosylation	Interactions Focus chain C Focus chain F Interactions & Density Focus chain C Focus chain F
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, E, G, H, I D, E, G, H, I, J, K	2		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Interactions & Density Focus chain D Focus chain E Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3TP Query on 3TP Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain T [auth B] MOL2 format, chain P [auth A] MOL2 format, chain T [auth B]	P [auth A], T [auth B]	(2S,3S)-3-{3-[4-(METHYLSULFONYL)PHENYL]-1,2,4-OXADIAZOL-5-YL}-1-OXO-1-PYRROLIDIN-1-YLBUTAN-2-AMINE C₁₇ H₂₂ N₄ O₄ S SQCDMTZMCHZYGO-FZMZJTMJSA-N		Interactions Focus chain P [auth A] Focus chain T [auth B] Interactions & Density Focus chain P [auth A] Focus chain T [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B]	L [auth A] M [auth A] N [auth A] Q [auth B] R [auth B] L [auth A], M [auth A], N [auth A], Q [auth B], R [auth B], S [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A]	O [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
3TP	PDBBind: 2HHA	IC50: 122 (nM) from 1 assay(s)
3TP	BindingDB: 2HHA	IC50: 122 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.233
R-Value Work: 0.185
R-Value Observed: 0.206
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.971	α = 90
b = 125.584	β = 90
c = 136.716	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-09-19

Deposition Author(s):

Scapin, G.

Revision History (Full details and data files)

Version 1.0: 2006-09-19
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-10-18
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: 2023-08-30
Changes: Data collection, Refinement description