An unbiased cell morphology-based screen for new, biologically active small molecules

Tanaka, M.; Bateman, R.; Rauh, D.; Vaisberg, E.; Ramachandani, S.; Zhang, C.; Hansen, K.C.; Burlingame, A.L.; Trautman, J.K.; Shokat, K.M.; Adams, C.L.

doi:10.2210/pdb1wma/pdb

Macromolecule Content

Total Structure Weight: 32994.14
Atom Count: 2485
Residue Count: 276
Unique protein chains: 1

1WMA

Crystal structure of human CBR1 in complex with Hydroxy-PP

DOI: 10.2210/pdb1WMA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)

Deposited: 2004-07-06 Released: 2005-04-26
Deposition Author(s): Rauh, D., Bateman, R., Shokat, K.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.24 Å
R-Value Free: 0.167

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

An unbiased cell morphology-based screen for new, biologically active small molecules

Tanaka, M., Bateman, R., Rauh, D., Vaisberg, E., Ramachandani, S., Zhang, C., Hansen, K.C., Burlingame, A.L., Trautman, J.K., Shokat, K.M., Adams, C.L.

(2005) Plos Biol. 3: 128-128

PubMed: 15799708 Search on PubMedSearch on PubMed Central
DOI: 10.1371/journal.pbio.0030128

PubMed Abstract:

We have implemented an unbiased cell morphology-based screen to identify small-molecule modulators of cellular processes using the Cytometrix (TM) automated imaging and analysis system. This assay format provides unbiased analysis of morphological effects induced by small molecules by capturing phenotypic readouts of most known classes of pharmacological agents and has the potential to read out pathways for which little is known. Four human-cancer cell lines and one noncancerous primary cell type were treated with 107 small molecules comprising four different protein kinase-inhibitor scaffolds. Cellular phenotypes induced by each compound were quantified by multivariate statistical analysis of the morphology, staining intensity, and spatial attributes of the cellular nuclei, microtubules, and Golgi compartments. Principal component analysis was used to identify inhibitors of cellular components not targeted by known protein kinase inhibitors. Here we focus on a hydroxyl-substituted analog (hydroxy-PP) of the known Src-family kinase inhibitor PP2 because it induced cell-specific morphological features distinct from all known kinase inhibitors in the collection. We used affinity purification to identify a target of hydroxy-PP, carbonyl reductase 1 (CBR1), a short-chain dehydrogenase-reductase. We solved the X-ray crystal structure of the CBR1/hydroxy-PP complex to 1.24 A resolution. Structure-based design of more potent and selective CBR1 inhibitors provided probes for analyzing the biological function of CBR1 in A549 cells. These studies revealed a previously unknown function for CBR1 in serum-withdrawal-induced apoptosis. Further studies indicate CBR1 inhibitors may enhance the effectiveness of anticancer anthracyclines. Morphology-based screening of diverse cancer cell types has provided a method for discovering potent new small-molecule probes for cell biological studies and anticancer drug candidates.

Organizational Affiliation:

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, USA.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Carbonyl reductase [NADPH] 1	A	276	Homo sapiens	Mutation(s): 0 Gene Names: CBR1 (CBR, CRN, SDR21C1) EC: 1.1.1.184
Find proteins for P16152 (Homo sapiens) Go to Gene View: CBR1 Go to UniProtKB: P16152
Protein Feature View Full Protein Feature View for P16152

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
P33 Query on P33 Download SDF File Download CCD File	A	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL HEPTAETHYLENE GLYCOL, PEG330 C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Ligand Interaction
SO4 Query on SO4 Download SDF File Download CCD File	A	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
PE5 Query on PE5 Download SDF File Download CCD File	A	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL, POLYETHYLENE GLYCOL PEG400 C₁₈ H₃₈ O₉ CUDPPTPIUWYGFI-UHFFFAOYSA-N		Ligand Interaction
AB3 Query on AB3 Download SDF File Download CCD File	A	3-(4-AMINO-1-TERT-BUTYL-1H-PYRAZOLO[3,4-D]PYRIMIDIN-3-YL)PHENOL C₁₅ H₁₇ N₅ O CPLGZXQPPYRNRC-UHFFFAOYSA-N		Ligand Interaction
NDP Query on NDP Download SDF File Download CCD File	A	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Ligand Interaction