3HAC

The structure of DPP-4 in complex with piperidine fused imidazopyridine 34

PDB DOI: https://doi.org/10.2210/pdb3HAC/pdb

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

Deposited: 2009-05-01 Released: 2009-07-21
Deposition Author(s): Scapin, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.205
R-Value Work: 0.171
R-Value Observed: 0.173

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.3 of the entry. See complete history.

Literature

Aminopiperidine-fused imidazoles as dipeptidyl peptidase-IV inhibitors

Edmondson, S.D., Mastracchio, A., Cox, J.M., Eiermann, G.J., He, H., Lyons, K.A., Patel, R.A., Patel, S.B., Petrov, A., Scapin, G., Wu, J.K., Xu, S., Zhu, B., Thornberry, N.A., Roy, R.S., Weber, A.E.

(2009) Bioorg Med Chem Lett 19: 4097-4101

PubMed: 19539471 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2009.06.011
Primary Citation of Related Structures:
3HAB, 3HAC

PubMed Abstract:
A new series of DPP-4 inhibitors derived from piperidine-fused benzimidazoles and imidazopyridines is described. Optimization of this class of DPP-4 inhibitors led to the discovery of imidazopyridine 34. The potency, selectivity, cross-species DMPK profiles, and in vivo efficacy of 34 is reported.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 174.32 kDa
Atom Count: 13,578
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 soluble form	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: 7	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-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F, G C, D, E, F, G, H, I, J, K	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F 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
361 Query on 361 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]	(7R,8R)-8-(2,4,5-trifluorophenyl)-6,7,8,9-tetrahydroimidazo[1,2-a:4,5-c']dipyridin-7-amine C₁₆ H₁₃ F₃ N₄ SOSYXEPELJIJHZ-RNCFNFMXSA-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
361	BindingDB: 3HAC	IC50: min: 8.3, max: 67 (nM) from 3 assay(s)
	BindingDB: 3HAC	EC50: 112 (nM) from 1 assay(s)
	PDBBind: 3HAC	IC50: 6.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.205
R-Value Work: 0.171
R-Value Observed: 0.173
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.12	α = 90
b = 125.496	β = 90
c = 136.902	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
REFMAC	refinement
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: 2009-07-21

Deposition Author(s):

Scapin, G.

Revision History (Full details and data files)

Version 1.0: 2009-07-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2021-10-13
Changes: Database references, Structure summary
Version 3.0: 2021-10-27
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
Version 3.1: 2023-06-21
Changes: Derived calculations
Version 3.2: 2023-09-20
Changes: Data collection, Refinement description
Version 3.3: 2024-11-06
Changes: Structure summary