8V6W | pdb_00008v6w

Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with compound 1

PDB DOI: https://doi.org/10.2210/pdb8V6W/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.228 (Depositor), 0.238 (DCC)
R-Value Work:
0.162 (Depositor), 0.172 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure-based development of IPMK kinase inhibitors.

Wang, H., Shears, S.B.

To be published.

Macromolecule Content

Total Structure Weight: 30.12 kDa
Atom Count: 2,073
Modeled Residue Count: 237
Deposited Residue Count: 261
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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: 2.7.1.151 (PDB Primary Data), 2.7.1.153 (UniProt), 2.7.1.140 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFU5 (Homo sapiens) Explore Q8NFU5 Go to UniProtKB: Q8NFU5
PHAROS: Q8NFU5 GTEx: ENSG00000151151
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NFU5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YHE (Subject of Investigation/LOI) Query on YHE Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(2E)-3-[3-(3,5-dimethylphenyl)-2,1-benzoxazol-5-yl]prop-2-enoic acid C₁₈ H₁₅ N O₃ GVBOPZONHGVWNG-GQCTYLIASA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.228 (Depositor), 0.238 (DCC)
R-Value Work: 0.162 (Depositor), 0.172 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.656	α = 90
b = 77.656	β = 90
c = 84.831	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-12-11

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.