8I7Z | pdb_00008i7z

The crystal structure of human abl1 kinase domain in complex with ABL1-B5

• PDB DOI: https://doi.org/10.2210/pdb8I7Z/pdb

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


• Deposited: 2023-02-02 Released: 2024-10-23 
• Deposition Author(s): Zhu, C., Zhang, Z.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Rationally designed BCR-ABL kinase inhibitors for improved leukemia treatment via covalent and pro-/dual-drug targeting strategies.

Sun, J., Lou, L., Zhu, C., Chen, P., Tang, G., Gu, M., Xia, S., Dong, X., Zhang, Z.M., Gao, L., Yao, S.Q., Xiao, Q.

(2024) J Adv Res 

• PubMed: 39255927 
• DOI: https://doi.org/10.1016/j.jare.2024.09.008
• Primary Citation of Related Structures:  
  8I7S, 8I7T, 8I7Z


• PubMed Abstract: 
  

  Chronic Myeloid Leukemia (CML) is a blood cancer that remains challenging to cure due to drug resistance and side effects from current BCR-ABL inhibitors. There is an urgent need for novel and more effective BCR-ABL targeting inhibitors and therapeutic strategies to combat this deadly disease. We disclose an "OH-implant" strategy to improve a noncovalent BCR-ABL inhibitor, PPY-A, by adding a hydroxyl group to its scaffold. By taking advantage of this OH "hot spot", we designed a panel of irreversible covalent kinase inhibitors and hypoxia-responsive pro-/dual-drugs, and their biological activities were studied in vitro, in cellulo and in vivo. The resulting compound B1 showed enhanced solubility and biological activity. B4 achieved sustained BCR-ABL inhibition by forming a stable covalent bond with ABL kinase. Hypoxia-responsive prodrug P1 and dual-drugs D1/D2/D3 demonstrated significant anti-tumor effects under hypoxic conditions. The in vivo studies using K562-xenografted mice showed that B1 displayed superior antitumor activity than PPY-A, while P1 and D3 offered better safety profiles alongside significant tumor control. We have successfully developed a chemical biology approach to convert a known noncovalent BCR-ABL inhibitor into more potent and safer inhibitors through covalent and pro-/dual-drug targeting strategies. Our "OH-implant" approach and the resulting drug design strategies have general applicability and hold promise for improvement the performance of various other reported drugs/drug candidates, thereby providing advanced medicines for disease treatment.

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Organizational Affiliation: 
• School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China. Electronic address: [e-mail].
School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China. Electronic address: [e-mail].
School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China. Electronic address: [e-mail].
School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China. Electronic address: [e-mail].
Department of Chemistry, National University of Singapore, Singapore 117543, Singapore. Electronic address: [e-mail].
School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China. Electronic address: [e-mail].
Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai 200444, China. Electronic address: [e-mail].
Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai 200444, China. Electronic address: [e-mail].
School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China. Electronic address: [e-mail].
School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China. Electronic address: [e-mail].
Department of Chemistry, National University of Singapore, Singapore 117543, Singapore. Electronic address: [e-mail].
School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China. Electronic address: [e-mail].

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.

Macromolecule Content 

• Total Structure Weight: 64.18 kDa 
• Atom Count: 4,513 
• Modeled Residue Count: 523 
• Deposited Residue Count: 544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase ABL1	A, B	272	Homo sapiens	Mutation(s): 0  Gene Names: ABL1, ABL, JTK7 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P00519 (Homo sapiens) Explore P00519  Go to UniProtKB:  P00519
PHAROS:  P00519 GTEx:  ENSG00000097007

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6CI (Subject of Investigation/LOI)	C [auth A], E [auth B]	5-[3-(2-methoxy-5-oxidanyl-phenyl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N,N-dimethyl-pyridine-3-carboxamide C22 H20 N4 O3 LEFHTGQOJNMOKU-UHFFFAOYSA-N
BAL (Subject of Investigation/LOI)	D [auth A]	BETA-ALANINE C3 H7 N O2 UCMIRNVEIXFBKS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.603	α = 90
b = 133.37	β = 90
c = 56.554	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-23 
Deposition Author(s): Zhu, C., Zhang, Z.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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