2AJL

X-ray Structure of Novel Biaryl-Based Dipeptidyl peptidase IV inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2AJL/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2005-08-02 Released: 2005-11-08 
• Deposition Author(s): Qiao, L., Baumann, C.A., Crysler, C.S., Ninan, N.S., Abad, M.C., Spurlino, J.C., DesJarlais, R.L., Kervinen, J., Neeper, M.P., Bayoumy, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.303 
• R-Value Work: 0.226 

Starting Model: experimental

Literature

Discovery, SAR, and X-ray structure of novel biaryl-based dipeptidyl peptidase IV inhibitors

Qiao, L., Baumann, C.A., Crysler, C.S., Ninan, N.S., Abad, M.C., Spurlino, J.C., Desjarlais, R.L., Kervinen, J., Neeper, M.P., Bayoumy, S.S., Williams, R., Deckman, I.C., Dasgupta, M., Reed, R.L., Huebert, N.D., Tomczuk, B.E., Moriarty, K.J.

(2006) Bioorg Med Chem Lett 16: 123-128

• PubMed: 16236500 
• DOI: https://doi.org/10.1016/j.bmcl.2005.09.037
• Primary Citation of Related Structures:  
  2AJL


• PubMed Abstract: 
  

  The discovery, SAR, and X-ray crystal structure of novel biarylaminoacyl-(S)-2-cyano-pyrrolidines and biarylaminoacylthiazolidines as potent inhibitors of dipeptidyl peptidase IV (DPP IV) are reported.

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Organizational Affiliation: 

Johnson and Johnson Pharmaceutical Research and Development, 665 Stockton Drive, Exton, PA 19341, USA.

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: 172.67 kDa 
• Atom Count: 12,558 
• Modelled Residue Count: 1,454 
• Deposited Residue Count: 1,456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A [auth I], B [auth J]	728	Homo sapiens	Mutation(s): 0  Gene Names: DPP4, ADCP2, CD26 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JNH	H [auth I], R [auth J]	1-[2-(S)-AMINO-3-BIPHENYL-4-YL-PROPIONYL]-PYRROLIDINE-2-(S)-CARBONITRILE C20 H25 N3 O MUUVLSCVDXKQQV-OALUTQOASA-N
NAG	C [auth I], D [auth I], E [auth I], F [auth I], G [auth I], I [auth J], J, K [auth J], L [auth J], M [auth J], N [auth J], O [auth J], P [auth J], Q [auth J]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
JNH	PDBBind:  2AJL	Ki: 13 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.303 
• R-Value Work: 0.226 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.279	α = 90
b = 126.877	β = 99.41
c = 110.828	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
CNS	refinement
PROTEUM PLUS	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-08 
Deposition Author(s): Qiao, L., Baumann, C.A., Crysler, C.S., Ninan, N.S., Abad, M.C., Spurlino, J.C., DesJarlais, R.L., Kervinen, J., Neeper, M.P., Bayoumy, S.S.

Revision History  

• Version 1.0: 2005-11-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary