6IBY

Human PFKFB3 in complex with a N-Aryl 6-Aminoquinoxaline inhibitor 6

• PDB DOI: https://doi.org/10.2210/pdb6IBY/pdb

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


• Deposited: 2018-12-01 Released: 2019-01-23 
• Deposition Author(s): Banaszak, K., Pawlik, H., Bialas, A., Fabritius, C.H., Nowak, M.
• Funding Organization(s): European Regional Development Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.232 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 51.07 kDa 
• Atom Count: 3,704 
• Modelled Residue Count: 428 
• Deposited Residue Count: 428 
• 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	428	Homo sapiens	Mutation(s): 0  Gene Names: PFKFB3 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HAT	B [auth A]	3-[[8-(1-methylindol-6-yl)quinoxalin-6-yl]amino]-~{N}-[(3~{S})-1-methylpyrrolidin-3-yl]pyridine-4-carboxamide C28 H27 N7 O JQYNBBAXGSXALE-FQEVSTJZSA-N
F6P	E [auth A]	6-O-phosphono-beta-D-fructofuranose C6 H13 O9 P BGWGXPAPYGQALX-ARQDHWQXSA-N
FLC	D [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
POP	C [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
PO4	G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
BME	F [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.232 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.532	α = 90
b = 102.532	β = 90
c = 253.658	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Banaszak, K., Pawlik, H., Bialas, A., Fabritius, C.H., Nowak, M.

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Funding Organization	Location	Grant Number
European Regional Development Fund		under The Operational Program Innovative Economy, 2007-2013, measure 1.4 (POIG.01.04.00-12-120/12-00)

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2019-02-13
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary