5AK0 | pdb_00005ak0

Human PFKFB3 in complex with an indole inhibitor 6

• PDB DOI: https://doi.org/10.2210/pdb5AK0/pdb

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


• Deposited: 2015-02-27 Released: 2015-04-22 
• Deposition Author(s): Boyd, S., Brookfield, J.L., Critchlow, S.E., Cumming, I.A., Curtis, N.J., Debreczeni, J.E., Degorce, S.L., Donald, C., Evans, N.J., Groombridge, S., Hopcroft, P., Jones, N.P., Kettle, J.G., Lamont, S., Lewis, H.J., MacFaull, P., McLoughlin, S.B., Rigoreau, L.J.M., Smith, J.M., St-Gallay, S., Stock, J.K., Wheatley, E.R., Winter, J., Wingfield, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.204 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Structure-Based Design of Potent and Selective Inhibitors of the Metabolic Kinase Pfkfb3.

Boyd, S., Brookfield, J.L., Critchlow, S.E., Cumming, I.A., Curtis, N.J., Debreczeni, J., Degorce, S.L., Donald, C., Evans, N.J., Groombridge, S., Hopcroft, P., Jones, N.P., Kettle, J.G., Lamont, S., Lewis, H.J., Macfaull, P., Mcloughlin, S.B., Rigoreau, L.J.M., Smith, J.M., St-Gallay, S., Stock, J.K., Turnbull, A.P., Wheatley, E.R., Winter, J., Wingfield, J.

(2015) J Med Chem 58: 3611

• PubMed: 25849762 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b00352
• Primary Citation Related Structures: 
  5AJV, 5AJW, 5AJX, 5AJY, 5AJZ, 5AK0


• PubMed Abstract: 
  

  A weak screening hit with suboptimal physicochemical properties was optimized against PFKFB3 kinase using critical structure-guided insights. The resulting compounds demonstrated high selectivity over related PFKFB isoforms and modulation of the target in a cellular context. A selected example demonstrated exposure in animals following oral dosing. Examples from this series may serve as useful probes to understand the emerging biology of this metabolic target.

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Organizational Affiliation: 
• †Oncology Innovative Medicines Unit, AstraZeneca, 35S47 Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom.
‡CRT Discovery Laboratories, Jonas Webb Building (B910), Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom.
§CRT Discovery Laboratories, Wolfson Institute for Biomedical Research, University College London, The Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom.

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: 60.64 kDa 
• Atom Count: 4,019 
• Modeled Residue Count: 442 
• Deposited Residue Count: 520 
• 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	520	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
8V1	F [auth A]	(2S)-N-[4-[1-METHYL-3-(1-METHYLPYRAZOL-4-YL)INDOL-5-YL]OXYPHENYL]PYRROLIDINE-2-CARBOXAMIDE C24 H25 N5 O2 JTIOFEOXCFFWJI-QFIPXVFZSA-N
F6P	E [auth A]	6-O-phosphono-beta-D-fructofuranose C6 H13 O9 P BGWGXPAPYGQALX-ARQDHWQXSA-N
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
PHS	B [auth A]	PHOSPHONIC ACID H3 O3 P ABLZXFCXXLZCGV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.204 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.42	α = 90
b = 103.42	β = 90
c = 260.71	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: 2015-04-22 
Deposition Author(s): Boyd, S., Brookfield, J.L., Critchlow, S.E., Cumming, I.A., Curtis, N.J., Debreczeni, J.E., Degorce, S.L., Donald, C., Evans, N.J., Groombridge, S., Hopcroft, P., Jones, N.P., Kettle, J.G., Lamont, S., Lewis, H.J., MacFaull, P., McLoughlin, S.B., Rigoreau, L.J.M., Smith, J.M., St-Gallay, S., Stock, J.K., Wheatley, E.R., Winter, J., Wingfield, J.

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release
  
• Version 1.1: 2015-05-13
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Structure summary