8ZML | pdb_00008zml

Structure of TNIK with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8ZML/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia phage EcSzw-2
• Mutation(s): No 


• Deposited: 2024-05-23 Released: 2025-05-28 
• Deposition Author(s): Fan, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.326 (Depositor), 0.323 (DCC) 
• R-Value Work: 
  0.256 (Depositor), 0.257 (DCC) 

Starting Model: experimental

Literature

Structure of TNIK with inhibitor

Fan, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.87 kDa 
• Atom Count: 5,144 
• Modeled Residue Count: 601 
• Deposited Residue Count: 606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAF2 and NCK-interacting protein kinase	A, B	303	Homo sapiens	Mutation(s): 0  Gene Names: TNIK, KIAA0551 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKE5 (Homo sapiens) Explore Q9UKE5  Go to UniProtKB:  Q9UKE5
PHAROS:  Q9UKE5 GTEx:  ENSG00000154310

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D8H (Subject of Investigation/LOI)	C [auth A], G [auth B]	Rentosertib C27 H30 F N7 O ZVDNXHUSIKGTSF-UHFFFAOYSA-N
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	F [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A, B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.326 (Depositor), 0.323 (DCC) 
• R-Value Work:  0.256 (Depositor), 0.257 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.889	α = 90
b = 89.595	β = 90
c = 97.577	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Fan, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release
  
• Version 1.1: 2025-11-19
  Changes: Derived calculations, Structure summary