3R02

The discovery of novel benzofuran-2-carboxylic acids as potent Pim-1 inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3R02/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-07 Released: 2011-05-11 
• Deposition Author(s): Xiang, Y., Hirth, B., Asmussen, G., Biemann, H.-P., Good, A., Fitzgerald, M., Gladysheva, T., Jancsics, K., Liu, J., Metz, M., Papoulis, A., Skerlj, R., Stepp, D.J., Wei, R.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.189 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Literature

The discovery of novel benzofuran-2-carboxylic acids as potent Pim-1 inhibitors.

Xiang, Y., Hirth, B., Asmussen, G., Biemann, H.P., Bishop, K.A., Good, A., Fitzgerald, M., Gladysheva, T., Jain, A., Jancsics, K., Liu, J., Metz, M., Papoulis, A., Skerlj, R., Stepp, J.D., Wei, R.R.

(2011) Bioorg Med Chem Lett 21: 3050-3056

• PubMed: 21507633 
• DOI: https://doi.org/10.1016/j.bmcl.2011.03.030
• Primary Citation of Related Structures:  
  3R00, 3R01, 3R02, 3R04


• PubMed Abstract: 
  

  Novel benzofuran-2-carboxylic acids, exemplified by 29, 38 and 39, have been discovered as potent Pim-1 inhibitors using fragment based screening followed by X-ray structure guided medicinal chemistry optimization. The compounds demonstrate potent inhibition against Pim-1 and Pim-2 in enzyme assays. Compound 29 has been tested in the Ambit 442 kinase panel and demonstrates good selectivity for the Pim kinase family. X-ray structures of the inhibitor/Pim-1 binding complex reveal important salt-bridge and hydrogen bond interactions mediated by the compound's carboxylic acid and amino groups.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Drug and Biomaterial R&D, Genzyme Corp., 153 Second Avenue, Waltham, MA 02451, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.04 kDa 
• Atom Count: 2,417 
• Modelled Residue Count: 271 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene serine/threonine-protein kinase pim-1	A	299	Homo sapiens	Mutation(s): 0  Gene Names: PIM1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens) Explore P11309  Go to UniProtKB:  P11309
PHAROS:  P11309 GTEx:  ENSG00000137193

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNM	B [auth A]	7-[(cis-4-aminocyclohexyl)amino]-5-bromo-1-benzofuran-2-carboxylic acid C15 H17 Br N2 O3 BLBAWGODFTZAEY-PHIMTYICSA-N
IMD	C [auth A], D [auth A], E [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Binding Affinity Annotations
ID	Source	Binding Affinity
UNM	BindingDB:  3R02	IC50: 1 (nM) from 1 assay(s)
	PDBBind:  3R02	IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.189 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.17	α = 90
b = 97.17	β = 90
c = 81.19	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-11 
Deposition Author(s): Xiang, Y., Hirth, B., Asmussen, G., Biemann, H.-P., Good, A., Fitzgerald, M., Gladysheva, T., Jancsics, K., Liu, J., Metz, M., Papoulis, A., Skerlj, R., Stepp, D.J., Wei, R.R.

Revision History  

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations