4JH0 | pdb_00004jh0

Crystal structure of dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2) (DPP-IV-WT) complex with bms-767778 AKA 2-(3-(aminomethyl)-4-(2,4- dichlorophenyl)-2-methyl-5-oxo-5,7-dihydro-6h-pyrrolo[3,4- b]pyridin-6-yl)-n,n-dimethylacetamide

• PDB DOI: https://doi.org/10.2210/pdb4JH0/pdb

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


• Deposited: 2013-03-04 Released: 2013-09-04 
• Deposition Author(s): Klei, H.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.272 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Literature

Optimization of Activity, Selectivity, and Liability Profiles in 5-Oxopyrrolopyridine DPP4 Inhibitors Leading to Clinical Candidate (Sa)-2-(3-(Aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl-5-oxo-5H-pyrrolo[3,4-b]pyridin-6(7H)-yl)-N,N-dimethylacetamide (BMS-767778).

Devasthale, P., Wang, Y., Wang, W., Fevig, J., Feng, J., Wang, A., Harrity, T., Egan, D., Morgan, N., Cap, M., Fura, A., Klei, H.E., Kish, K., Weigelt, C., Sun, L., Levesque, P., Moulin, F., Li, Y.X., Zahler, R., Kirby, M.S., Hamann, L.G.

(2013) J Med Chem 56: 7343-7357

• PubMed: 23964740 
• DOI: https://doi.org/10.1021/jm4008906
• Primary Citation Related Structures: 
  4JH0, 4LKO


• PubMed Abstract: 
  

  Optimization of a 5-oxopyrrolopyridine series based upon structure-activity relationships (SARs) developed from our previous efforts on a number of related bicyclic series yielded compound 2s (BMS-767778) with an overall activity, selectivity, efficacy, PK, and developability profile suitable for progression into the clinic. SAR in the series and characterization of 2s are described.

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Organizational Affiliation: 
• Metabolic Diseases Chemistry, ‡Metabolic Diseases Biology, §Pharmaceutical Candidate Optimization, ∥Protein Science and Structure, ⊥Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development , Princeton, New Jersey 08543-5400, United States.

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: 169.74 kDa 
• Atom Count: 12,054 
• Modeled 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  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 GTEx:  ENSG00000197635

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1MD	C [auth A], D [auth B]	2-[3-(aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl-5-oxo-5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-N,N-dimethylacetamide C19 H20 Cl2 N4 O2 PECDPZCIECMGCM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.272 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.311	α = 90
b = 67.105	β = 90
c = 423.771	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Klei, H.E.

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2013-10-09
  Changes: Database references
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary