3HAB | pdb_00003hab

The structure of DPP4 in complex with piperidine fused benzimidazole 25

PDB DOI: https://doi.org/10.2210/pdb3HAB/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: 2.10 Å
R-Value Free:
0.211 (Depositor), 0.219 (DCC)
R-Value Work:
0.169 (Depositor), 0.184 (DCC)
R-Value Observed:
0.171 (Depositor)

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 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: 174.47 kDa
Atom Count: 13,644
Modeled Residue Count: 1,456
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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
677 Query on 677 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,3R)-7-(methylsulfonyl)-3-(2,4,5-trifluorophenyl)-1,2,3,4-tetrahydropyrido[1,2-a]benzimidazol-2-amine C₁₈ H₁₆ F₃ N₃ O₂ S HJJAYSSCWGUPKO-ABAIWWIYSA-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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.211 (Depositor), 0.219 (DCC)
R-Value Work: 0.169 (Depositor), 0.184 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.908	α = 90
b = 125.645	β = 90
c = 136.941	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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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: Non-polymer description, 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: 2024-11-20
Changes: Structure summary