Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 104.15 kDa 
• Atom Count: 6613 
• Residue Count: 867 
• Unique protein chains: 1

5HG1

Crystal Structure of Human Hexokinase 2 with cmpd 1, a C-2-substituted glucosamine

• DOI: 10.2210/pdb5HG1/pdb

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


• Deposited: 2016-01-07 Released: 2016-03-30 
• Deposition Author(s): Campobasso, N., Zhao, B., Smallwood, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 0.266 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

Literature

Discovery of a Novel 2,6-Disubstituted Glucosamine Series of Potent and Selective Hexokinase 2 Inhibitors.

Lin, H., Zeng, J., Xie, R., Schulz, M.J., Tedesco, R., Qu, J., Erhard, K.F., Mack, J.F., Raha, K., Rendina, A.R., Szewczuk, L.M., Kratz, P.M., Jurewicz, A.J., Cecconie, T., Martens, S., McDevitt, P.J., Martin, J.D., Chen, S.B., Jiang, Y., Nickels, L., Schwartz, B.J., Smallwood, A., Zhao, B., Campobasso, N., Qian, Y., Briand, J., Rominger, C.M., Oleykowski, C., Hardwicke, M.A., Luengo, J.I.

(2016) ACS Med Chem Lett 7: 217-222

• PubMed: 26985301 
• DOI: 10.1021/acsmedchemlett.5b00214
• Primary Citation of Related Structures:  
  5HG1, 5HEX, 5HFU


• PubMed Abstract: 
  

A novel series of potent and selective hexokinase 2 (HK2) inhibitors, 2,6-disubstituted glucosamines, has been identified based on HTS hits, exemplified by compound 1. Inhibitor-bound crystal structures revealed that the HK2 enzyme could adopt an "induced-fit" conformation. The SAR study led to the identification of potent HK2 inhibitors, such as compound 34 with greater than 100-fold selectivity over HK1. Compound 25 inhibits in situ glycolysis in a UM-UC-3 bladder tumor cell line via (13)CNMR measurement of [3-(13)C]lactate produced from [1,6-(13)C2]glucose added to the cell culture.

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Organizational Affiliation: 

Cancer Metabolism Chemistry; Cancer Metabolism Biology; and Platform Technology & Sciences, GlaxoSmithKline , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexokinase-2	A	922	Homo sapiens	Mutation(s): 0  Gene Names: HK2 EC: 2.7.1.1
Find proteins for P52789 (Homo sapiens) Explore P52789  Go to UniProtKB:  P52789
NIH Common Fund Data Resources
PHAROS:  P52789 GTEx:  ENSG00000159399

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
62C	A	2-deoxy-2-{[(2E)-3-(3,4-dichlorophenyl)prop-2-enoyl]amino}-alpha-D-glucopyranose C15 H17 Cl2 N O6 ZBHWRKZTEDNOAJ-GJAUZLMESA-N
BG6	A	6-O-phosphono-beta-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-VFUOTHLCSA-N
FLC	A	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 0.266 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.12	α = 90
b = 165.12	β = 90
c = 126.478	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-01-07 
• Released Date: 2016-03-30 
Deposition Author(s): Campobasso, N., Zhao, B., Smallwood, A.

Revision History 

• Version 1.0: 2016-03-30
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary