2JID

Human Dipeptidyl peptidase IV in complex with 1-(3,4-Dimethoxy-phenyl) -3-m-tolyl-piperidine-4-ylamine

• PDB DOI: https://doi.org/10.2210/pdb2JID/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2007-02-28 Released: 2008-05-27 
• Deposition Author(s): Hennig, M., Stihle, M., Luebbers, T., Thoma, R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.303 
• R-Value Work: 0.223 
• R-Value Observed: 0.227 

Literature

1,3-Disubstituted 4-Aminopiperidines as Useful Tools in the Optimization of the 2-Aminobenzo[A]Quinolizine Dipeptidyl Peptidase Iv Inhibitors.

Lubbers, T., Bohringer, M., Gobbi, L., Hennig, M., Hunziker, D., Kuhn, B., Loffler, B., Mattei, P., Narquizian, R., Peters, J., Ruff, Y., Wessel, H.P., Wyss, P.

(2007) Bioorg Med Chem Lett 17: 2966

• PubMed: 17418568 
• DOI: https://doi.org/10.1016/j.bmcl.2007.03.072
• Primary Citation of Related Structures:  
  2JID


• PubMed Abstract: 
  

  In a search for novel DPP-IV inhibitors, 2-aminobenzo[a]quinolizines were identified as submicromolar HTS hits. Due to the difficult synthetic access to this compound class, 1,3-disubstituted 4-aminopiperidines were used as model compounds for optimization. The developed synthetic methodology and the SAR could be transferred to the 2-aminobenzo[a]quinolizine series, leading to highly active DPP-IV inhibitors.

---

Organizational Affiliation: 

Discovery Research, Pharmaceutical Division, F. Hoffmann-La Roche Ltd, CH-4070 Basel, Switzerland. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 172.84 kDa 
• Atom Count: 12,214 
• Modelled Residue Count: 1,456 
• Deposited Residue Count: 1,472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIPEPTIDYL PEPTIDASE 4	A, B	736	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: 1		Go to GlyGen: P27487-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GVB	G [auth A], L [auth B]	(3R,4S)-1-(3,4-DIMETHOXYPHENYL)-3-(3-METHYLPHENYL)PIPERIDIN-4-AMINE C20 H26 N2 O2 DQJXBZGPJVSWFI-ROUUACIJSA-N
NAG	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.303 
• R-Value Work: 0.223 
• R-Value Observed: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.251	α = 90
b = 66.821	β = 90
c = 423.948	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Hennig, M., Stihle, M., Luebbers, T., Thoma, R.

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2012-08-29
  Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Structure summary