4JH0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.272 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/jm4008906
  • Primary Citation of 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.


  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4
A, B
728Homo sapiensMutation(s): 0 
Gene Names: DPP4ADCP2CD26
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27487
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1MD
Query on 1MD

Download Ideal Coordinates CCD File 
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), 0.270 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.311α = 90
b = 67.105β = 90
c = 423.771γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
CNXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 1MDClick on this verticalbar to view details

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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