8UM5 | pdb_00008um5

X-ray structure of human SHIP1 Ptase-C2 domains covalently bound to TREAT-AD (TAD) compound TAD-58547

• PDB DOI: https://doi.org/10.2210/pdb8UM5/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-10-17 Released: 2024-10-23 
• Deposition Author(s): Mesecar, A.D., Hamdani, A.K.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of human SHIP1 Ptase-C2 domains covalently bound to TREAT-AD (TAD) compound TAD-58547

Hamdani, A.K., Mesecar, A.D.

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: 53.37 kDa 
• Atom Count: 4,141 
• Modelled Residue Count: 451 
• Deposited Residue Count: 463 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1	A	463	Homo sapiens	Mutation(s): 0  Gene Names: INPP5D EC: 3.1.3.56 (UniProt), 3.1.3.86 (UniProt), 3.1.3.36 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92835 (Homo sapiens) Explore Q92835  Go to UniProtKB:  Q92835
PHAROS:  Q92835 GTEx:  ENSG00000168918

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X3F (Subject of Investigation/LOI)	B [auth A]	5-(1,4-oxazepan-4-yl)-6-propanoylpyridine-2-carbonitrile C14 H17 N3 O2 QAYKYSCIOWYYNH-UHFFFAOYSA-N
DMS	C [auth A], D [auth A], E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.643	α = 90
b = 82.266	β = 108.55
c = 59.749	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-23 
Deposition Author(s): Mesecar, A.D., Hamdani, A.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	1U54AG065181
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30CA023168

Revision History  

• Version 1.0: 2024-10-23
  Type: Initial release