8HMT | pdb_00008hmt

The complex of ACK1 with the inhibitor 2-142

• PDB DOI: https://doi.org/10.2210/pdb8HMT/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2022-12-05 Released: 2023-12-13 
• Deposition Author(s): Zhu, S., Xiaoyun, X.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free: 
  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

The complex of ACK1 with the inhibitor 2-142

Zhu, S., Xiaoyun, X.Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 127.26 kDa 
• Atom Count: 8,730 
• Modeled Residue Count: 1,063 
• Deposited Residue Count: 1,092 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Activated CDC42 kinase 1	A, B, C, D	273	Homo sapiens	Mutation(s): 0  Gene Names: TNK2, ACK1 EC: 2.7.10.2 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q07912 (Homo sapiens) Explore Q07912  Go to UniProtKB:  Q07912
PHAROS:  Q07912 GTEx:  ENSG00000061938

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LWX (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	6-(2-bromophenyl)-2-[[3-methyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-8-[[(2S)-oxolan-2-yl]methyl]pyrido[2,3-d]pyrimidin-7-one C30 H33 Br N6 O2 MMGYUMBPTKHMTO-QHCPKHFHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.17 Å
• R-Value Free:  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.71	α = 90
b = 133.01	β = 90.35
c = 110.667	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Zhu, S., Xiaoyun, X.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81903539

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release