4N8E | pdb_00004n8e

DPP4 complexed with compound 12a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.218 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4N8E

Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Discovery of C-(1-aryl-cyclohexyl)-methylamines as selective, orally available inhibitors of dipeptidyl peptidase IV.

Namoto, K.Sirockin, F.Ostermann, N.Gessier, F.Flohr, S.Sedrani, R.Gerhartz, B.Trappe, J.Hassiepen, U.Duttaroy, A.Ferreira, S.Sutton, J.M.Clark, D.E.Fenton, G.Beswick, M.Baeschlin, D.K.

(2014) Bioorg Med Chem Lett 24: 731-736

  • DOI: https://doi.org/10.1016/j.bmcl.2013.12.118
  • Primary Citation Related Structures: 
    4N8D, 4N8E

  • PubMed Abstract: 

    The successful launches of dipeptidyl peptidase IV (DPP IV) inhibitors as oral anti-diabetics warrant and spur the further quest for additional chemical entities in this promising class of therapeutics. Numerous pharmaceutical companies have pursued their proprietary candidates towards the clinic, resulting in a large body of published chemical structures associated with DPP IV. Herein, we report the discovery of a novel chemotype for DPP IV inhibition based on the C-(1-aryl-cyclohexyl)-methylamine scaffold and its optimization to compounds which selectively inhibit DPP IV at low-nM potency and exhibit an excellent oral pharmacokinetic profile in the rat.


  • Organizational Affiliation
    • Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland. Electronic address: kenji.namoto@novartis.com.

Macromolecule Content 

  • Total Structure Weight: 176.45 kDa 
  • Atom Count: 13,353 
  • Modeled Residue Count: 1,461 
  • Deposited Residue Count: 1,480 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4
A, B
740Homo 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
Glycosylation
Glycosylation Sites: 6Go to GlyGen: P27487-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G21381MC
GlyCosmos: G21381MC
GlyGen: G21381MC

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2KV

Query on 2KV



Download:Ideal Coordinates CCD File
M [auth A],
W [auth B]
1-[cis-4-(aminomethyl)-4-(3-chlorophenyl)cyclohexyl]piperidin-2-one
C18 H25 Cl N2 O
HPAJLBAQCKXNNT-SAABIXHNSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth A]
K [auth A]
L [auth A]
T [auth B]
U [auth B]
J [auth A],
K [auth A],
L [auth A],
T [auth B],
U [auth B],
V [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.218 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.09α = 90
b = 122.048β = 90
c = 191.348γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-11-20
    Changes: Data collection, Database references, Structure summary