4JPG

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

Structural Biology Knowledgebase: 4JPG SBKB.org


Experimental Data Snapshot

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

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JPG

Classification: TRANSFERASE / TRANSFERASE ACTIVATOR

Total Structure Weight: 245727.59

Macromolecule Entities
Molecule Chains Length Organism Details
Pyruvate kinase isozymes M1/M2 A, B, C, D 556 Homo sapiens EC#: 2.7.1.40 IUBMB
Gene Name(s): PKM Gene View OIP3 PK2 PK3 PKM2

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FBP
Query on FBP

A, B, C, D BETA-FRUCTOSE-1,6-DIPHOSPHATE
FRUCTOSE-1,6-BISPHOSPHATE (Synonym)
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
1OX
Query on 1OX

B, D 2-(1H-benzimidazol-1-ylmethyl)-4H-pyrido[1,2- a]pyrimidin-4-one
C16 H12 N4 O
BCWFSHAZZLFCIE-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.177
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 80.97 α = 90.00
b = 153.61 β = 103.45
c = 93.48 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

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

Revision History

No revisions since initial release