4D4M | pdb_00004d4m

human PFKFB3 in complex with a pyrrolopyrimidone compound

• PDB DOI: https://doi.org/10.2210/pdb4D4M/pdb

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


• Deposited: 2014-10-29 Released: 2016-01-20 
• Deposition Author(s): Stgallay, S.A., Bennett, N., Critchlow, S., Davies, G., Debreczeni, J.E., Evans, N., Holdgate, G., Jones, N.P., Leach, L., Maman, S., McLoughlin, S., Preston, M., Rigoreau, L., Thomas, A., Walker, G., Walsch, J., Ward, R.A., Wheatley, E., Winter, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.209 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Identifying a Novel Series of Pfkfb3 Inhibitors as a Metabolic Approach to Treating Cancer from Hts, Biophysical and Biochemical Methods

Stgallay, S.A., Bennett, N., Critchlow, S., Davies, G., Debreczeni, J.E., Evans, N., Holdgate, G., Jones, N.P., Leach, L., Maman, S., Mcloughlin, S., Preston, M., Rigoreau, L., Thomas, A., Walker, G., Walsch, J., Ward, R.A., Wheatley, E., Winter, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.96 kDa 
• Atom Count: 3,889 
• Modeled Residue Count: 439 
• Deposited Residue Count: 449 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE 3	A	449	Homo sapiens	Mutation(s): 0  EC: 2.7.1.105 (PDB Primary Data), 3.1.3.46 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16875 (Homo sapiens) Explore Q16875  Go to UniProtKB:  Q16875
PHAROS:  Q16875 GTEx:  ENSG00000170525

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BKV	F [auth A]	7-(4-bromophenyl)-5-phenyl-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one C18 H12 Br N3 O PNDQJUVRRFIFTM-UHFFFAOYSA-N
F6P	E [auth A]	6-O-phosphono-beta-D-fructofuranose C6 H13 O9 P BGWGXPAPYGQALX-ARQDHWQXSA-N
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
PHS	D [auth A]	PHOSPHONIC ACID H3 O3 P ABLZXFCXXLZCGV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.209 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.62	α = 90
b = 102.62	β = 90
c = 257.66	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Stgallay, S.A., Bennett, N., Critchlow, S., Davies, G., Debreczeni, J.E., Evans, N., Holdgate, G., Jones, N.P., Leach, L., Maman, S., McLoughlin, S., Preston, M., Rigoreau, L., Thomas, A., Walker, G., Walsch, J., Ward, R.A., Wheatley, E., Winter, J.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Structure summary