3KWF

human DPP-IV with carmegliptin (S)-1-((2S,3S,11bS)-2-Amino-9,10-dimethoxy-1,3,4,6,7,11b-hexahydro-2H-pyrido[2,1-a]isoquinolin-3-yl)-4-fluoromethyl-pyrrolidin-2-one

• PDB DOI: https://doi.org/10.2210/pdb3KWF/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.246 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Discovery of carmegliptin: A potent and long-acting dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes.

Mattei, P., Boehringer, M., Di Giorgio, P., Fischer, H., Hennig, M., Huwyler, J., Kocer, B., Kuhn, B., Loeffler, B.M., Macdonald, A., Narquizian, R., Rauber, E., Sebokova, E., Sprecher, U.

(2010) Bioorg Med Chem Lett 20: 1109-1113

• PubMed: 20031405 
• DOI: https://doi.org/10.1016/j.bmcl.2009.12.024
• Primary Citation of Related Structures:  
  3KWF, 3OC0


• PubMed Abstract: 
  

  Design, synthesis, and SAR are described for a class of DPP-IV inhibitors based on aminobenzo[a]quinolizines with non-aromatic substituents in the S1 specificity pocket. One representative thereof, carmegliptin (8p), was chosen for clinical development. Its X-ray structure in complex with the enzyme and early efficacy data in animal models of type 2 diabetes are also presented.

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Organizational Affiliation: 

F Hoffmann-La Roche Ltd, Pharma Research, 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 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 170.56 kDa 
• Atom Count: 12,464 
• 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	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
B1Q	E [auth A], H [auth B]	(4S)-1-[(2S,3S,11bS)-2-amino-9,10-dimethoxy-1,3,4,6,7,11b-hexahydro-2H-pyrido[2,1-a]isoquinolin-3-yl]-4-(fluoromethyl)pyrrolidin-2-one C20 H28 F N3 O3 GUYMHFIHHOEFOA-ZCPGHIKRSA-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
B1Q	PDBBind:  3KWF	IC50: 6.8 (nM) from 1 assay(s)
	BindingDB:  3KWF	IC50: 6.8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.246 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.626	α = 90
b = 69.541	β = 90
c = 423.039	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Hennig, M., Stihle, M., Thoma, R.

Revision History  

• Version 1.0: 2010-01-12
  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: 2024-11-27
  Changes: Data collection, Database references, Structure summary