8V76 | pdb_00008v76

Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with compound 12

• PDB DOI: https://doi.org/10.2210/pdb8V76/pdb

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


• Deposited: 2023-12-04 Released: 2024-12-11 
• Deposition Author(s): Wang, H., Shears, S.B.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.209 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Structure-based development of IPMK kinase inhibitors.

Wang, H., Shears, S.B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.3 kDa 
• Atom Count: 2,152 
• Modeled Residue Count: 234 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol polyphosphate multikinase	A	261	Homo sapiens	Mutation(s): 0  Gene Names: IPMK, IMPK EC: 2.7.1.140 (PDB Primary Data), 2.7.1.151 (PDB Primary Data), 2.7.1.153 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFU5 (Homo sapiens) Explore Q8NFU5  Go to UniProtKB:  Q8NFU5
PHAROS:  Q8NFU5 GTEx:  ENSG00000151151

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YIU (Subject of Investigation/LOI)	B [auth A]	N-{(3P)-3-[(5P)-5-(2H-tetrazol-5-yl)-2,1-benzoxazol-3-yl]phenyl}cyclopentanecarboxamide C20 H18 N6 O2 OFSLXIACVHOLTC-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.209 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.024	α = 90
b = 78.024	β = 90
c = 85.495	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Wang, H., Shears, S.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	1ZIAES080046

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release