Skip to main content

 1RWQ | pdb_00001rwq

Human Dipeptidyl peptidase IV in complex with 5-aminomethyl-6-(2,4-dichloro-phenyl)-2-(3,5-dimethoxy-phenyl)-pyrimidin-4-ylamine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.290 (Depositor) 
  • R-Value Work: 
    0.239 (Depositor) 
  • R-Value Observed: 
    0.241 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1RWQ

This is version 1.4 of the entry. See complete history. 

Literature

Aminomethylpyrimidines as novel DPP-IV inhibitors: a 10(5)-fold activity increase by optimization of aromatic substituents

Peters, J.U., Weber, S., Kritter, S., Weiss, P., Wallier, A., Boehringer, M., Hennig, M., Kuhn, B., Loeffler, B.M.

(2004) Bioorg Med Chem Lett 14: 1491-1493

  • DOI: https://doi.org/10.1016/j.bmcl.2004.01.019
  • Primary Citation Related Structures: 
    1RWQ

  • PubMed Abstract: 

    The influence of aromatic substitution on a newly discovered class of inhibitors of dipeptidyl peptidase IV was investigated. A 10(5)-fold increase in potency was achieved by the optimization of aromatic substituents in a parallel chemistry program. The observed SAR could be explained by an X-ray structure of the protein-ligand complex.

    • Organizational Affiliation: 
    • Pharma Division, Preclinical Research, F. Hoffmann-La Roche Ltd, CH-4070 Basel, Switzerland. jens-uwe.peters@roche.com

Macromolecule Content 

  • Total Structure Weight: 171.51 kDa 
  • Atom Count: 12,190 
  • Modeled Residue Count: 1,456 
  • Deposited Residue Count: 1,456 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase IV
A, B
728Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27487
Glycosylation
Glycosylation Sites: 4
Go to GlyGen: P27487-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5AP

Query on 5AP


Download:Ideal Coordinates CCD File
G [auth A],
L [auth B]		5-(AMINOMETHYL)-6-(2,4-DICHLOROPHENYL)-2-(3,5-DIMETHOXYPHENYL)PYRIMIDIN-4-AMINE
C19 H18 Cl2 N4 O2
RCJFINNFYUNFGH-UHFFFAOYSA-N
NAG

Query on NAG


Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.290 (Depositor) 
  • R-Value Work:  0.239 (Depositor) 
  • R-Value Observed: 0.241 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.676α = 90
b = 69.141β = 90
c = 422.559γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-12-25
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary