6BSK | pdb_00006bsk

Human PIM1 kinase in complex with compound 12b

PDB DOI: https://doi.org/10.2210/pdb6BSK/pdb

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

Deposited: 2017-12-03 Released: 2018-03-21
Deposition Author(s): Ferguson, A.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.196 (Depositor), 0.182 (DCC)
R-Value Work:
0.170 (Depositor), 0.168 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Discovery of 2,6-disubstituted pyrazine derivatives as inhibitors of CK2 and PIM kinases.

Gingipalli, L., Block, M.H., Bao, L., Cooke, E., Dakin, L.A., Denz, C.R., Ferguson, A.D., Johannes, J.W., Larsen, N.A., Lyne, P.D., Pontz, T.W., Wang, T., Wu, X., Wu, A., Zhang, H.J., Zheng, X., Dowling, J.E., Lamb, M.L.

(2018) Bioorg Med Chem Lett 28: 1336-1341

PubMed: 29559278 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2018.03.018
Primary Citation Related Structures:
6BSK

PubMed Abstract:
The design and synthesis of a novel series of 2,6-disubstituted pyrazine derivatives as CK2 kinase inhibitors is described. Structure-guided optimization of a 5-substituted-3-thiophene carboxylic acid screening hit (3a) led to the development of a lead compound (12b), which shows inhibition in both enzymatic and cellular assays. Subsequent design and hybridization efforts also led to the unexpected identification of analogs with potent PIM kinase activity (14f).

Organizational Affiliation

Chemistry, Oncology, IMED Biotech Unit, AstraZeneca, Boston, USA; 35 Gatehouse Drive, Waltham, MA 02451, USA. Electronic address: lakshmaiah.gingipalli@astrazeneca.com.

Macromolecule Content

Total Structure Weight: 32.72 kDa
Atom Count: 2,361
Modeled Residue Count: 273
Deposited Residue Count: 276
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	276	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11309
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MVG Query on MVG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	4-{6-[6-(propan-2-ylamino)-1H-indazol-1-yl]pyrazin-2-yl}benzoic acid C₂₁ H₁₉ N₅ O₂ RJXWGPDMMDILGJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
MVG	BindingDB: 6BSK	IC50: 120 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.196 (Depositor), 0.182 (DCC)
R-Value Work: 0.170 (Depositor), 0.168 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.035	α = 90
b = 97.035	β = 90
c = 81.13	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-03-21

Deposition Author(s):

Ferguson, A.D.

Revision History (Full details and data files)

Version 1.0: 2018-03-21
Type: Initial release
Version 1.1: 2018-04-04
Changes: Data collection, Database references
Version 1.2: 2018-04-25
Changes: Data collection, Database references
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description