3RO4 | pdb_00003ro4

X-ray Structure of Ketohexokinase in complex with an indazole compound derivative

• PDB DOI: https://doi.org/10.2210/pdb3RO4/pdb

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


• Deposited: 2011-04-25 Released: 2011-08-03 
• Deposition Author(s): Abad, M.C., Gibbs, A.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.297 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.261 (Depositor) 

Starting Model: experimental

Literature

Optimization of a pyrazole hit from FBDD into a novel series of indazoles as ketohexokinase inhibitors.

Zhang, X., Song, F., Kuo, G.H., Xiang, A., Gibbs, A.C., Abad, M.C., Sun, W., Kuo, L.C., Sui, Z.

(2011) Bioorg Med Chem Lett 21: 4762-4767

• PubMed: 21767952 
• DOI: https://doi.org/10.1016/j.bmcl.2011.06.067
• Primary Citation of Related Structures:  
  3RO4


• PubMed Abstract: 
  

  A series of indazoles have been discovered as KHK inhibitors from a pyrazole hit identified through fragment-based drug discovery (FBDD). The optimization process guided by both X-ray crystallography and solution activity resulted in lead-like compounds with good pharmaceutical properties.

---

Organizational Affiliation: 

Johnson & Johnson Pharmaceutical Research and Development, Welsh & McKean Roads, PO Box 776, Spring House, PA 19477, United States. [e-mail]

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: 68.68 kDa 
• Atom Count: 4,545 
• Modeled Residue Count: 587 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LJ9	D [auth B]	3-ethyl-6-[(3aR,6aS)-hexahydropyrrolo[3,4-c]pyrrol-2(1H)-yl]-1-phenyl-1H-indazole C21 H24 N4 JRGJWNYNELQBIY-IYBDPMFKSA-N
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
LJ9	BindingDB:  3RO4	IC50: min: 590, max: 5360 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.297 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.61	α = 90
b = 86.034	β = 90
c = 139.792	γ = 90

Software Package:

Software Name	Purpose
JDirector	data collection
PHENIX	model building
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-03 
Deposition Author(s): Abad, M.C., Gibbs, A.C.

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2012-05-23
  Changes: Database references
• Version 1.2: 2012-12-05
  Changes: Other
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description