3KWJ

Structure of human DPP-IV with (2S,3S,11bS)-3-(3-Fluoromethyl-phenyl)-9,10-dimethoxy-1,3,4,6,7,11b-hexahydro-2H-pyrido[2,1-a]isoquinolin-2-ylamine

• PDB DOI: https://doi.org/10.2210/pdb3KWJ/pdb

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


• Deposited: 2009-12-01 Released: 2010-09-15 
• Deposition Author(s): Hennig, M., Stihle, M., Thoma, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.276 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 

Literature

Aryl- and heteroaryl-substituted aminobenzo[a]quinolizines as dipeptidyl peptidase IV inhibitors.

Boehringer, M., Fischer, H., Hennig, M., Hunziker, D., Huwyler, J., Kuhn, B., Loeffler, B.M., Luebbers, T., Mattei, P., Narquizian, R., Sebokova, E., Sprecher, U., Wessel, H.P.

(2010) Bioorg Med Chem Lett 20: 1106-1108

• PubMed: 20031408 
• DOI: https://doi.org/10.1016/j.bmcl.2009.12.025
• Primary Citation of Related Structures:  
  3KWJ


• PubMed Abstract: 
  

  Synthesis and SAR are described for a structurally distinct class of DPP-IV inhibitors based on aminobenzo[a]quinolizines bearing (hetero-)aromatic substituents in the S1 specificity pocket. The m-(fluoromethyl)-phenyl derivative (S,S,S)-2g possesses the best fit in the S1 pocket. However, (S,S,S)-2i, bearing a more hydrophilic 5-methyl-pyridin-2-yl residue as substituent for the S1 pocket, displays excellent in vivo activity and superior drug-like properties.

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Organizational Affiliation: 

F Hoffmann-La Roche Ltd, Pharma Research, CH-4070 Basel, Switzerland.

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: 170.55 kDa 
• Atom Count: 12,060 
• Modelled Residue Count: 1,456 
• Deposited Residue Count: 1,456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4 soluble form	A, B	728	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
23Q	E [auth A], H [auth B]	(2S,3S,11bS)-3-[3-(fluoromethyl)phenyl]-9,10-dimethoxy-1,3,4,6,7,11b-hexahydro-2H-pyrido[2,1-a]isoquinolin-2-amine C22 H27 F N2 O2 OQMKJZHTWPQABR-AABGKKOBSA-N
NAG	C [auth A], D [auth A], F [auth B], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
23Q	BindingDB:  3KWJ	IC50: 0.5 (nM) from 1 assay(s)
	PDBBind:  3KWJ	IC50: 0.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.276 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.199	α = 90
b = 68.957	β = 90
c = 421.562	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Hennig, M., Stihle, M., Thoma, R.

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2020-09-09
  Changes: Structure summary
• Version 1.4: 2024-11-27
  Changes: Data collection, Database references, Structure summary