9D03 | pdb_00009d03

Co-crystal structure of circularly permuted human taspase-1 bound to ligand SMDC1014689 1-(ethenesulfonyl)-4-{[3-fluoro-4-(trifluoromethoxy)phenyl]methyl}piperazine

PDB DOI: https://doi.org/10.2210/pdb9D03/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-08-06 Released: 2025-08-13
Deposition Author(s): Delker, S.L., Edwards, T.E., Abendroth, J.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.201 (Depositor), 0.202 (DCC)
R-Value Work:
0.159 (Depositor), 0.162 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Co-crystal structure of circularly permuted human taspase-1 bound to ligand SMDC1014689 1-(ethenesulfonyl)-4-{[3-fluoro-4-(trifluoromethoxy)phenyl]methyl}piperazine

Delker, S.L., Edwards, T.E., Abendroth, J.

To be published.

Macromolecule Content

Total Structure Weight: 71.58 kDa
Atom Count: 4,463
Modeled Residue Count: 621
Deposited Residue Count: 678
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Threonine aspartase subunit beta,Threonine aspartase subunit alpha	A, B	339	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H6P5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
R1M (Subject of Investigation/LOI) Query on R1M Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	1-(ethenylsulfonyl)-4-{[3-fluoro-4-(trifluoromethoxy)phenyl]methyl}piperazine C₁₄ H₁₆ F₄ N₂ O₃ S WHVCBNZSLXXMMA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	D [auth A], F [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]