9E6U | pdb_00009e6u

Crystal structure of human Taspase1 in complex with ligand SMDC1041556

• PDB DOI: https://doi.org/10.2210/pdb9E6U/pdb

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


• Deposited: 2024-10-31 Released: 2025-11-05 
• Deposition Author(s): Doamekpor, S.K., Hamilton, K., Choi, P.H., Tong, L.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.275 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Design and mechanism of potent inhibitors for the Mixed Lineage Leukemia (MLL) activating protease, Taspase-1

Doamekpor, S.K., Hamilton, K., Choi, P.H., Tong, L., Delker, S., Waterson, A., Neitz, J., Sambucetti, L., Arkin, M.

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 84.66 kDa 
• Atom Count: 4,467 
• Modeled Residue Count: 607 
• Deposited Residue Count: 788 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Threonine aspartase 1	A, B	394	Homo sapiens	Mutation(s): 0  Gene Names: TASP1, C20orf13 EC: 3.4.25
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H6P5 (Homo sapiens) Explore Q9H6P5  Go to UniProtKB:  Q9H6P5
PHAROS:  Q9H6P5 GTEx:  ENSG00000089123

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U47 (Subject of Investigation/LOI)	D [auth A], F [auth B]	(2R)-4-(ethenylsulfonyl)-1-{[3-fluoro-4-(trifluoromethoxy)phenyl]methyl}-2-{[(1H-1,2,3-triazol-4-yl)methoxy]methyl}piperazine C18 H21 F4 N5 O4 S FWYJSNSBSOKARB-OAHLLOKOSA-N
NA	C [auth A], E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.275 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.705	α = 90
b = 93.902	β = 90
c = 105.218	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Doamekpor, S.K., Hamilton, K., Choi, P.H., Tong, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release