2QTB

Human dipeptidyl peptidase iv/cd26 in complex with a 4-aryl cyclohexylalanine inhibitor

PDB DOI: https://doi.org/10.2210/pdb2QTB/pdb

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

Deposited: 2007-08-01 Released: 2007-11-06
Deposition Author(s): Scapin, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.228
R-Value Work: 0.187

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

Literature

4-Arylcyclohexylalanine analogs as potent, selective, and orally active inhibitors of dipeptidyl peptidase IV.

Kaelin, D.E., Smenton, A.L., Eiermann, G.J., He, H., Leiting, B., Lyons, K.A., Patel, R.A., Patel, S.B., Petrov, A., Scapin, G., Wu, J.K., Thornberry, N.A., Weber, A.E., Duffy, J.L.

(2007) Bioorg Med Chem Lett 17: 5806-5811

PubMed: 17851076 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2007.08.049
Primary Citation of Related Structures:
2QT9, 2QTB

PubMed Abstract:
A novel series of 4-arylcyclohexylalanine DPP-4 inhibitors was synthesized and tested for inhibitory activity as well as selectivity over the related proline-specific enzymes DPP-8 and DPP-9. Optimization of this series led to 28 (DPP-4 IC(50)=4.8 nM), which showed an excellent pharmacokinetic profile across several preclinical species. Evaluation of 28 in an oral glucose tolerance test demonstrated that this compound effectively reduced glucose excursion in lean mice.

Organizational Affiliation

Department of Medicinal Chemistry, Merck Research Laboratories, Rahway, NJ 07065, USA. david_kaelin@merck.com

Macromolecule Content

Total Structure Weight: 182.83 kDa
Atom Count: 13,252
Modelled Residue Count: 1,456
Deposited Residue Count: 1,532
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	766	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: 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 [auth L], F [auth O]	2		N-Glycosylation	Interactions Focus chain C [auth L] Focus chain F [auth O] Interactions & Density Focus chain C [auth L] Focus chain F [auth O]
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 M], E [auth C], G [auth P], H [auth Q], I [auth R], D [auth M], E [auth C], G [auth P], H [auth Q], I [auth R], J [auth S], K [auth T]	2		N-Glycosylation	Interactions Focus chain D [auth M] Focus chain E [auth C] Focus chain G [auth P] Focus chain H [auth Q] Focus chain I [auth R] Focus chain J [auth S] Focus chain K [auth T] Interactions & Density Focus chain D [auth M] Focus chain E [auth C] Focus chain G [auth P] Focus chain H [auth Q] Focus chain I [auth R] Focus chain J [auth S] Focus chain K [auth T]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
474 Query on 474 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] mmCIF format, chain P [auth A] mmCIF format, chain T [auth B]	P [auth A], T [auth B]	(2S,3S)-3-AMINO-4-(3,3-DIFLUOROPYRROLIDIN-1-YL)-N,N-DIMETHYL-4-OXO-2-(TRANS-4-[1,2,4]TRIAZOLO[1,5-A]PYRIDIN-6-YLCYCLOHEXYL)BUTANAMIDE C₂₂ H₃₀ F₂ N₆ O₂ JNAZOMVWUGPITI-LNMJFAINSA-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] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF 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] mmCIF 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
474	PDBBind: 2QTB	IC50: 4.8 (nM) from 1 assay(s)
474	BindingDB: 2QTB	IC50: min: 4.8, max: 130 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.228
R-Value Work: 0.187
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.863	α = 90
b = 125.629	β = 90
c = 136.806	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
CNX	phasing
CNX	refinement

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: Non-polymer description, 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: 2023-08-30
Changes: Data collection, Refinement description
Version 2.3: 2024-10-30
Changes: Structure summary