Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 60641.70 
• Atom Count: 3632 
• Residue Count: 520 
• Unique protein chains: 1

5AK0

Human PFKFB3 in complex with an indole inhibitor 6

• DOI: 10.2210/pdb5AK0/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• 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 
• R-Value Work: 0.179 

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: 10.1021/acs.jmedchem.5b00352
• Primary Citation of Related Structures:  
  5AJZ, 5AJY, 5AJX, 5AJW, 5AJV


• 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: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
6-PHOSPHOFRUCTO-2-KINASE/FRUCTOSE-2,6-BISPHOSPHATASE 3	A	520	Homo sapiens	Mutation(s): 0  Gene Names: PFKFB3
Find proteins for Q16875 (Homo sapiens) Go to Gene View: PFKFB3 Go to UniProtKB:  Q16875

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
8V1	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
PHS	A	PHOSPHONIC ACID H3 O3 P ABLZXFCXXLZCGV-UHFFFAOYSA-N
F6P	A	FRUCTOSE-6-PHOSPHATE C6 H13 O9 P BGWGXPAPYGQALX-ARQDHWQXSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
8V1	IC50: 21 - 9710 nM (100) BINDINGDB
8V1	IC50: 21 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 103.420	α = 90.00
b = 103.420	β = 90.00
c = 260.710	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-02-27 
• 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
  Type: Database references