8OMK

hKHK-C in complex with ADP & fructose 1-phosphate

• PDB DOI: https://doi.org/10.2210/pdb8OMK/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-31 Released: 2024-01-10 
• Deposition Author(s): Ebenhoch, R., Pautsch, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.219 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 

Literature

Discovery of BI-9787, a Potent Zwitterionic KHK-Inhibitor with Oral Bioavailability

Heine, N., Weber, A., Pautsch, A., Gottschling, D., Upheus, I., Baur, M., Ebenhoch, R., Nosse, B., Kley, 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.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 69.46 kDa 
• Atom Count: 4,924 
• Modelled Residue Count: 600 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketohexokinase	A, B	313	Homo sapiens	Mutation(s): 0  Gene Names: KHK EC: 2.7.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P50053 (Homo sapiens) Explore P50053  Go to UniProtKB:  P50053
PHAROS:  P50053 GTEx:  ENSG00000138030

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	D [auth A], E [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
F1X (Subject of Investigation/LOI)	C [auth A]	1-O-phosphono-beta-D-fructofuranose C6 H13 O9 P RHKKZBWRNHGJEZ-ARQDHWQXSA-N
SO4	F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.219 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.809	α = 90
b = 85.818	β = 90
c = 137.24	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
XDS	data reduction
BALBES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-10 
Deposition Author(s): Ebenhoch, R., Pautsch, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-01-10
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Experimental preparation
• Version 1.2: 2024-01-24
  Changes: Data collection