245,392
Structures from the PDB archive

1,068,577
Computed Structure Models (CSM)

2J2I|pdb_00002j2i

Crystal Structure of the humab PIM1 in complex with LY333531

PDB DOI: https://doi.org/10.2210/pdb2J2I/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2006-08-16 Released: 2007-02-13
Deposition Author(s): Debreczeni, J.E.,Bullock, A.N.,von Delft, F.,Sundstrom, M.,Arrowsmith, C.,Edwards, A.,Weigelt, J.,Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model:experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.7 of the entry. See complete history.

Literature

A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases.

Fedorov, O., Marsden, B., Pogacic, V., Rellos, P., Muller, S., Bullock, A.N., Schwaller, J., Sundstrom, M., Knapp, S.

(2007) Proc Natl Acad Sci U S A 104: 20523-20528

PubMed: 18077363 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.0708800104
Primary Citation of Related Structures:
2J2I

PubMed Abstract:
Protein kinases play a pivotal role in cell signaling, and dysregulation of many kinases has been linked to disease development. A large number of kinase inhibitors are therefore currently under investigation in clinical trials, and so far seven inhibitors have been approved as anti-cancer drugs. In addition, kinase inhibitors are widely used as specific probes to study cell signaling, but systematic studies describing selectivity of these reagents across a panel of diverse kinases are largely lacking. Here we evaluated the specificity of 156 validated kinase inhibitors, including inhibitors used in clinical trials, against 60 human Ser/Thr kinases using a thermal stability shift assay. Our analysis revealed many unexpected cross-reactivities for inhibitors thought to be specific for certain targets. We also found that certain combinations of active-site residues in the ATP-binding site correlated with the detected ligand promiscuity and that some kinases are highly sensitive to inhibition using diverse chemotypes, suggesting them as preferred intervention points. Our results uncovered also inhibitor cross-reactivities that may lead to alternate clinical applications. For example, LY333'531, a PKCbeta inhibitor currently in phase III clinical trials, efficiently inhibited PIM1 kinase in our screen, a suggested target for treatment of leukemia. We determined the binding mode of this inhibitor by x-ray crystallography and in addition showed that LY333'531 induced cell death and significantly suppressed growth of leukemic cells from acute myeloid leukemia patients.

Organizational Affiliation

Structural Genomics Consortium, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, United Kingdom.

Macromolecule Content

Total Structure Weight: 36.07 kDa
Atom Count: 2,445
Modeled Residue Count: 273
Deposited Residue Count: 312
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1	A [auth B]	312	Homo sapiens	Mutation(s): 1 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11309
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LY4 Query on LY4 Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	(9R)-9-[(DIMETHYLAMINO)METHYL]-6,7,10,11-TETRAHYDRO-9H,18H-5,21:12,17-DIMETHENODIBENZO[E,K]PYRROLO[3,4-H][1,4,13]OXADIAZACYCLOHEXADECINE-18,20-DIONE C₂₈ H₂₈ N₄ O₃ ZCBUQCWBWNUWSU-SFHVURJKSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B Interactions & Density Focus chain B

Binding Affinity Annotations
ID	Source	Binding Affinity
LY4	BindingDB: 2J2I	Kd: min: 50, max: 270 (nM) from 3 assay(s)
LY4	BindingDB: 2J2I	IC50: 200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.200 (Depositor), 0.200 (DCC)
R-Value Work: 0.179 (Depositor), 0.180 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.157	α = 90
b = 98.157	β = 90
c = 80.366	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-02-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-02-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2018-01-24
Changes: Structure summary
Version 1.3: 2018-02-28
Changes: Database references, Source and taxonomy
Version 1.4: 2018-04-04
Changes: Data collection
Version 1.5: 2019-03-06
Changes: Data collection, Experimental preparation
Version 1.6: 2019-05-08
Changes: Data collection, Experimental preparation
Version 1.7: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary