9YU9 | pdb_00009yu9

The crystal structure of human abl1 kinase domain in complex with PH-ELV-1022

• PDB DOI: https://doi.org/10.2210/pdb9YU9/pdb

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


• Deposited: 2025-10-22 Released: 2026-10-28 
• Deposition Author(s): Chao, A., DuPrez, K.T., Lyssikatos, J.P., Kintz, S., Han, F.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.285 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.256 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Starting Model: experimental

Literature

Relcobatinib, a highly selective ATP-competitive ABL1 tyrosine kinase inhibitor for the treatment of chronic myeloid leukemia.

Gross, S.D., Eide, C.A., Burkard, M.R., Reister Schultz, A., Chao, A., DuPrez, K.T., Han, F., Broad, A.J., Reuther, D., Zhang, Y., Aslan, J.E., McCarty, O.J.T., Aujay, M.A., Kintz, S., Druker, B.J., Lyssikatos, J.P.

(2026) Leukemia 

• PubMed: 42977784 
• DOI: https://doi.org/10.1038/s41375-026-03184-x
• Primary Citation Related Structures: 
  9YU9, 9YUB


• PubMed Abstract: 
  

  Relcobatinib (ELVN-001) is a next-generation, investigational, BCR::ABL1 active-site tyrosine kinase inhibitor (TKI) with a unique P-loop folded-in binding mode designed to deliver best-in-class efficacy with an improved tolerability profile over that of other TKIs for the treatment of chronic myeloid leukemia (CML). We demonstrate that relcobatinib has marked selectivity for BCR::ABL1, without inhibition of off-target kinases implicated in toxicities related to other TKIs. Relcobatinib exhibited greater selectivity than other active-site TKIs and demonstrated robust activity in vitro against native BCR::ABL1 and a broad range of clinically relevant TKI-resistant mutants. A BCR::ABL1 mouse xenograft model of human CML showed marked anti-tumor activity with relcobatinib as monotherapy, and, in combination with asciminib, showed further durable tumor regression, supporting the complementary mechanism of action between an active-site TKI and an allosteric inhibitor. Collectively, the preclinical profile of relcobatinib, marked by selective BCR::ABL1 targeting, supports its potential to improve efficacy and tolerability in the treatment of CML and other BCR::ABL1-driven malignancies, as monotherapy and in combination with an allosteric inhibitor.

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Organizational Affiliation: 
• Enliven Therapeutics, Burlingame, CA, USA. [e-mail].
Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
Enliven Therapeutics, Burlingame, CA, USA.
Structure Based Design, Inc., San Diego, CA, USA.
Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.

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: 68.43 kDa 
• Atom Count: 4,517 
• Modeled Residue Count: 541 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase ABL1	A, B	290	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
GTEx:  ENSG00000097007

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CZ6 (Subject of Investigation/LOI)	C [auth A], J [auth B]	relcobatinib C18 H18 F N5 O3 SULRARRXFNUQFC-MNOVXSKESA-N
GOL	H [auth A], I [auth A], K [auth B], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
PTR	A, B	TYR	Phosphorylation	C9 H12 N O6 P

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.285 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.256 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.291	α = 90
b = 117.277	β = 90
c = 126.36	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Chao, A., DuPrez, K.T., Lyssikatos, J.P., Kintz, S., Han, F.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release
  
• Version 2.0: 2026-11-11
  Changes: Database references, Derived calculations, Non-polymer description, Structure summary