1RWQ

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

• PDB DOI: https://doi.org/10.2210/pdb1RWQ/pdb

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


• Deposited: 2003-12-17 Released: 2004-12-17 
• Deposition Author(s): Hennig, M., Thoma, R., Stihle, M.

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Experimental Data Snapshot

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

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

• PubMed: 15006388 
• DOI: https://doi.org/10.1016/j.bmcl.2004.01.019
• Primary Citation of 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.

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Organizational Affiliation: 

Pharma Division, Preclinical Research, F. Hoffmann-La Roche Ltd, CH-4070 Basel, Switzerland. [e-mail]

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: 171.51 kDa 
• Atom Count: 12,190 
• Modelled 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 IV	A, B	728	Homo sapiens	Mutation(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
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: P27487-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5AP	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	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

Binding Affinity Annotations
ID	Source	Binding Affinity
5AP	PDBBind:  1RWQ	IC50: 0.1 (nM) from 1 assay(s)
	BindingDB:  1RWQ	IC50: 0.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.290 
• R-Value Work: 0.239 
• R-Value Observed: 0.241 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.676	α = 90
b = 69.141	β = 90
c = 422.559	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-17 
Deposition Author(s): Hennig, M., Thoma, R., Stihle, M.

Revision History  

• 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