4A5S | pdb_00004a5s

CRYSTAL STRUCTURE OF HUMAN DPP4 IN COMPLEX WITH A NOVAL HETEROCYCLIC DPP4 INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb4A5S/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-10-28 Released: 2012-02-08 
• Deposition Author(s): Ostermann, N., Kroemer, M., Zink, F., Gerhartz, B., Sutton, J.M., Clark, D.E., Dunsdon, S.J., Fenton, G., Fillmore, A., Harris, N.V., Higgs, C., Hurley, C.A., Krintel, S.L., MacKenzie, R.E., Duttaroy, A., Gangl, E., Maniara, W., Sedrani, R., Namoto, K., Sirockin, F., Trappe, J., Hassiepen, U., Baeschlin, D.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.179 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Novel Heterocyclic Dpp-4 Inhibitors for the Treatment of Type 2 Diabetes.

Sutton, J.M., Clark, D.E., Dunsdon, S.J., Fenton, G., Fillmore, A., Harris, N.V., Higgs, C., Hurley, C.A., Krintel, S.L., Mackenzie, R.E., Duttaroy, A., Gangl, E., Maniara, W., Sedrani, R., Namoto, K., Ostermann, N., Gerhartz, B., Sirockin, F., Trappe, J., Hassiepen, U., Baeschlin, D.K.

(2012) Bioorg Med Chem Lett 22: 1464

• PubMed: 22177783 
• DOI: https://doi.org/10.1016/j.bmcl.2011.11.054
• Primary Citation Related Structures: 
  4A5S


• PubMed Abstract: 
  

  Novel deazaxanthine-based DPP-4 inhibitors have been identified that are potent (IC(50) <10nM) and highly selective versus other dipeptidyl peptidases. Their synthesis and SAR are reported, along with initial efforts to improve the PK profile through decoration of the deazaxanthine core. Optimisation of compound 3a resulted in the identification of compound (S)-4i, which displayed an improved in vitro and ADME profile. Further enhancements to the PK profile were possible by changing from the deazahypoxanthine to the deazaxanthine template, culminating in compound 12g, which displayed good ex vivo DPP-4 inhibition and a superior PK profile in rat, suggestive of once daily dosing in man.

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Organizational Affiliation: 
• Argenta Discovery 2009 Ltd, Harlow CM19 5TR, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 176.78 kDa 
• Atom Count: 13,990 
• Modeled Residue Count: 1,462 
• Deposited Residue Count: 1,480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIPEPTIDYL PEPTIDASE 4 SOLUBLE FORM	A, B	740	Homo sapiens	Mutation(s): 0  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
Glycosylation
Glycosylation Sites: 6		Go to GlyGen: P27487-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G21381MC GlyCosmos: G21381MC GlyGen: G21381MC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N7F	D [auth A], N [auth B]	6-[(3S)-3-AMINOPIPERIDIN-1-YL]-5-BENZYL-4-OXO-3-(QUINOLIN-4-YLMETHYL)-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDINE-7-CARBONITRILE C29 H27 N7 O WRJSBPQWADEDBH-QFIPXVFZSA-N
NAG	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
N7F	BindingDB:  4A5S	IC50: 17 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.179 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.183	α = 90
b = 121.424	β = 90
c = 190.699	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-08 
Deposition Author(s): Ostermann, N., Kroemer, M., Zink, F., Gerhartz, B., Sutton, J.M., Clark, D.E., Dunsdon, S.J., Fenton, G., Fillmore, A., Harris, N.V., Higgs, C., Hurley, C.A., Krintel, S.L., MacKenzie, R.E., Duttaroy, A., Gangl, E., Maniara, W., Sedrani, R., Namoto, K., Sirockin, F., Trappe, J., Hassiepen, U., Baeschlin, D.K.

Revision History  

• Version 1.0: 2012-02-08
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary