6HD4: ABL1

ABL1 in complex with compound 7 and imatinib (sti-571). Determined by X-ray diffraction at 2.03 Å resolution. Released 24 Oct 2018.

Method: X-ray diffraction
Resolution: 2.03 Å
Organism: Mus musculus
Chains: 2
Atoms: 5,239
Mol. weight: 69.49 kDa
Ligands: STI, FYW
Released: 24 Oct 2018

Explore 6HD4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6HD4 contains 42 α-helices and 24 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	255	1	1
α-helix	258-260	3
β-strand	261-266	6	1
α-helix	267-270	4
β-strand	275-280	6	1
α-helix	281-283	3
β-strand	285-290	6	1
α-helix	299-311	13
β-strand	317	1	2
α-helix	318-319	2
β-strand	320-324	5	1
α-helix	330	1
β-strand	331-335	5	1
β-strand	340-341	2	2
α-helix	342-348	7
α-helix	356-375	20
α-helix	385-387	3
β-strand	388-390	3	2
α-helix	392-394	3
β-strand	396-398	3	2
β-strand	413-415	3	3
β-strand	418-420	3	3
α-helix	422-424	3
α-helix	427-432	6
α-helix	437-452	16
α-helix	456-457	2
α-helix	464-472	9
α-helix	477-480	4
α-helix	485-494	10
α-helix	499-501	3
α-helix	503-504	2
α-helix	505-515	11
α-helix	521-528	8

Chain B: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	255	1	4
α-helix	258-260	3
β-strand	261-266	6	4
α-helix	267-270	4
β-strand	275-280	6	4
β-strand	285-291	7	4
α-helix	299-310	12
β-strand	317	1	5
α-helix	318-319	2
β-strand	320-324	5	4
α-helix	330	1
β-strand	331-335	5	4
β-strand	340-341	2	5
α-helix	342-348	7
α-helix	356-375	20
α-helix	385-387	3
β-strand	388-390	3	5
α-helix	392-394	3
β-strand	396-398	3	5
β-strand	413-415	3	6
β-strand	418-420	3	6
α-helix	422-424	3
α-helix	427-432	6
α-helix	437-452	16
α-helix	456-457	2
α-helix	464-466	3
α-helix	467-472	6
α-helix	477-480	4
α-helix	485-494	10
α-helix	499-501	3
α-helix	503-504	2
α-helix	505-513	9
α-helix	521-528	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein kinase ABL1	A, B	protein	293	Mus musculus	P00520 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6HD4_1 Tyrosine-protein kinase ABL1 (chains A, B)
GAMDPSSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEE
FLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVSAVVLLY
MATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFP
IKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPE
GCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKELGKRGT

Ligands and cofactors

ID	Name	Formula	Copies
STI	4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-yla…	C29 H31 N7 O	2
FYW	6-[(3~{R})-3-oxidanylpyrrolidin-1-yl]-5-pyrimidin-5-yl-~{N}-[4-(trifluoromethyl…	C21 H18 F3 N5 O3	2

Water and common crystallization additives (CL, GOL) are not listed.

Primary citation

Discovery of Asciminib (ABL001), an Allosteric Inhibitor of the Tyrosine Kinase Activity of BCR-ABL1. Schoepfer, J., Jahnke, W., Berellini, G. et al. J Med Chem (2018) 61:8120-8135. DOI 10.1021/acs.jmedchem.8b01040 · PubMed

Other PDB entries of the same protein (UniProt P00520 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KFA 1.22 Å, Structural analysis of DFG-in and DFG-out dual Src-Abl inhibitors sharing a common vinyl…
3K5V 1.74 Å, Structure of Abl kinase in complex with imatinib and GNF-2
1OPJ 1.75 Å, Structural basis for the auto-inhibition of c-Abl tyrosine kinase
1OPK 1.8 Å, Structural basis for the auto-inhibition of c-Abl tyrosine kinase
3MS9 1.8 Å, ABL kinase in complex with imatinib and a fragment (FRAG1) in the myristate pocket
5IH2 1.8 Å, Structure, thermodynamics, and the role of conformational dynamics in the interactions…
3IK3 1.9 Å, AP24534, a Pan-BCR-ABL Inhibitor for Chronic Myeloid Leukemia, Potently Inhibits the…
3KF4 1.9 Å, Structural analysis of DFG-in and DFG-out dual Src-Abl inhibitors sharing a common vinyl…
2QOH 1.95 Å, Crystal Structure of Abl kinase bound with PPY-A
2Z60 1.95 Å, Crystal Structure of the T315I Mutant of Abl kinase bound with PPY-A
3MSS 1.95 Å, Abl kinase in complex with imatinib and fragment (FRAG2) in the myristate site
3OY3 1.95 Å, Crystal structure of ABL T315I mutant kinase domain bound with a DFG-out inhibitor AP24589

Browse structure collections

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