4LKO

Crystal structure of human DPP-IV in complex with BMS-744891


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1021/jm4008906
  • Primary Citation of Related Structures:  
    4LKO, 4JH0

  • 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, ...

    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.


    Related Citations: 
    • Structural basis of proline-specific exopeptidase activity as observed in human dipeptidyl peptidase-IV.
      Thoma, R., Loffler, B., Stihle, M., Huber, W., Ruf, A., Hennig, M.
      (2003) Structure 11: 947

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4 AB728Homo sapiensMutation(s): 0 
Gene Names: DPP4ADCP2CD26
EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens)
Explore P27487 
Go to UniProtKB:  P27487
NIH Common Fund Data Resources
PHAROS:  P27487
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1WH
Query on 1WH

Download Ideal Coordinates CCD File 
A, B
3-(aminomethyl)-4-(2,4-dichlorophenyl)-6-(2-methoxyethyl)-2-methyl-6,7-dihydro-5H-pyrrolo[3,4-b]pyridin-5-one
C18 H19 Cl2 N3 O2
LKKWOSVPEMTNNP-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1WHKi :  6   nM  PDBBind
1WHKi:  8.300000190734863   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.9α = 90
b = 68.3β = 90
c = 421.5γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNXphasing
CNXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-07-08 
  • 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