4MBL | pdb_00004mbl

Discovery of Pyrazolo[1,5a]pyrimidine-based Pim1 Inhibitors

PDB DOI: https://doi.org/10.2210/pdb4MBL/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-08-19 Released: 2013-09-11
Deposition Author(s): Azevedo, R., Fischmann, T.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.242 (Depositor), 0.250 (DCC)
R-Value Work:
0.201 (Depositor), 0.210 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of pyrazolo[1,5-a]pyrimidine-based Pim inhibitors: A template-based approach.

Dwyer, M.P., Keertikar, K., Paruch, K., Alvarez, C., Labroli, M., Poker, C., Fischmann, T.O., Mayer-Ezell, R., Bond, R., Wang, Y., Azevedo, R., Guzi, T.J.

(2013) Bioorg Med Chem Lett 23: 6178-6182

PubMed: 24091081 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2013.08.110
Primary Citation of Related Structures:
4MBI, 4MBL

PubMed Abstract:
The synthesis and hit-to-lead SAR development from a pyrazolo[1,5-a]pyrimidine-derived hit 5 to the identification of a series of potent, pan-Pim inhibitors such as 11j are described.

Organizational Affiliation

Department of Chemical Research, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, United States. Electronic address: michael.dwyer@merck.com.

Macromolecule Content

Total Structure Weight: 34.2 kDa
Atom Count: 2,257
Modelled Residue Count: 274
Deposited Residue Count: 293
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	293	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11309
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
26L Query on 26L Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(1R,2R)-N-[3-(naphthalen-2-yl)pyrazolo[1,5-a]pyrimidin-5-yl]cyclohexane-1,2-diamine C₂₂ H₂₃ N₅ LODPYXJMYAQIRB-WOJBJXKFSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
26L	BindingDB: 4MBL	IC50: 2.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.242 (Depositor), 0.250 (DCC)
R-Value Work: 0.201 (Depositor), 0.210 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.56	α = 90
b = 98.56	β = 90
c = 80.859	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
BUSTER	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-09-11

Deposition Author(s):

Azevedo, R.

Fischmann, T.O.

Revision History (Full details and data files)

Version 1.0: 2013-09-11
Type: Initial release
Version 1.1: 2013-10-30
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations