4JPG

2-((1H-benzo[d]imidazol-1-yl)methyl)-4H-pyrido[1,2-a]pyrimidin-4-ones as Novel PKM2 Activators

PDB DOI: https://doi.org/10.2210/pdb4JPG/pdb

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

Deposited: 2013-03-19 Released: 2013-05-22
Deposition Author(s): Greasley, S.E., Hickey, M., Phonephaly, H., Cronin, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.219
R-Value Work: 0.177
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 245.73 kDa
Atom Count: 16,344
Modelled Residue Count: 2,059
Deposited Residue Count: 2,224
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase isozymes M1/M2	A, B, C, D	556	Homo sapiens	Mutation(s): 0 Gene Names: PKM, OIP3, PK2, PK3, PKM2 EC: 2.7.1.40
UniProt & NIH Common Fund Data Resources
Find proteins for P14618 (Homo sapiens) Explore P14618 Go to UniProtKB: P14618
PHAROS: P14618 GTEx: ENSG00000067225
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14618
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FBP Query on FBP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain H [auth C] SDF format, chain I [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth D]	E [auth A], F [auth B], H [auth C], I [auth D]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain I [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain I [auth D]
1OX Query on 1OX Download Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain G [auth B] MOL2 format, chain J [auth D] MOL2 format, chain G [auth B]	G [auth B], J [auth D]	2-(1H-benzimidazol-1-ylmethyl)-4H-pyrido[1,2-a]pyrimidin-4-one C₁₆ H₁₂ N₄ O BCWFSHAZZLFCIE-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain J [auth D] Interactions & Density Focus chain G [auth B] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.219
R-Value Work: 0.177
R-Value Observed: 0.180
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.971	α = 90
b = 153.613	β = 103.45
c = 93.479	γ = 90

Software Package:

Software Name	Purpose
MxDC	data collection
ARP	model building
BUSTER	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-05-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-22
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2024-02-28
Changes: Advisory, Data collection, Database references, Structure summary

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4JPG

2-((1H-benzo[d]imidazol-1-yl)methyl)-4H-pyrido[1,2-a]pyrimidin-4-ones as Novel PKM2 Activators

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)