5I7U

Human DPP4 in complex with a novel tricyclic hetero-cycle inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 


Literature

Discovery of Novel Tricyclic Heterocycles as Potent and Selective DPP-4 Inhibitors for the Treatment of Type 2 Diabetes.

Wu, W.L., Hao, J., Domalski, M., Burnett, D.A., Pissarnitski, D., Zhao, Z., Stamford, A., Scapin, G., Gao, Y.D., Soriano, A., Kelly, T.M., Yao, Z., Powles, M.A., Chen, S., Mei, H., Hwa, J.

(2016) ACS Med Chem Lett 7: 498-501

  • DOI: https://doi.org/10.1021/acsmedchemlett.6b00027
  • Primary Citation of Related Structures:  
    5I7U

  • PubMed Abstract: 

    • In our efforts to develop second generation DPP-4 inhibitors, we endeavored to identify distinct structures with long-acting (once weekly) potential. Taking advantage of X-ray cocrystal structures of sitagliptin and other DPP-4 inhibitors, such as alogliptin and linagliptin bound to DPP-4, and aided by molecular modeling, we designed several series of heterocyclic compounds as initial targets ...

    In our efforts to develop second generation DPP-4 inhibitors, we endeavored to identify distinct structures with long-acting (once weekly) potential. Taking advantage of X-ray cocrystal structures of sitagliptin and other DPP-4 inhibitors, such as alogliptin and linagliptin bound to DPP-4, and aided by molecular modeling, we designed several series of heterocyclic compounds as initial targets. During their synthesis, an unexpected chemical transformation provided a novel tricyclic scaffold that was beyond our original design. Capitalizing on this serendipitous discovery, we have elaborated this scaffold into a very potent and selective DPP-4 inhibitor lead series, as highlighted by compound 17c.

    Organizational Affiliation: 

    Department of Lead Optimization Chemistry, Department of Structural Chemistry, Department of Pharmacology, and Department of Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories , 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4
A, B
728Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27487
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D 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
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6AJ
Query on 6AJ
Download Ideal Coordinates CCD File 
M [auth A],
R [auth B]		2-({2-[(3R)-3-aminopiperidin-1-yl]-5-methyl-6,9-dioxo-5,6,7,9-tetrahydro-1H-imidazo[1,2-a]purin-1-yl}methyl)-4-fluorobenzonitrile
C21 H21 F N8 O2
KMOYVYIQCXEQDG-OAHLLOKOSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
N [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
6AJ BindingDB:  5I7U IC50: 1.7 (nM) from 1 assay(s)
Binding MOAD:  5I7U IC50: 1.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.553α = 90
b = 126.545β = 90
c = 137.854γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2016-06-08 
    • Deposition Author(s): Scapin, G.

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary