3DK3: Mutant ABL kinase domain

Crystal structure of mutant ABL kinase domain in complex with small molecule fragment. Determined by X-ray diffraction at 2.02 Å resolution. Released 29 Jul 2008.

Method: X-ray diffraction
Resolution: 2.02 Å
Organism: Mus musculus
Chains: 2
Atoms: 4,631
Mol. weight: 68.72 kDa
Ligands: SX7
Released: 29 Jul 2008

Explore 3DK3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DK3 contains 43 α-helices and 28 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: 22 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	236	1	1
α-helix	239-241	3
β-strand	242-247	6	1
α-helix	249-251	3
β-strand	256-261	6	1
α-helix	262-264	3
β-strand	266-272	7	1
α-helix	280-290	11
β-strand	298	1	2
α-helix	299-300	2
β-strand	301-305	5	1
α-helix	311	1
β-strand	312-316	5	1
β-strand	322	1	2
α-helix	323-329	7
α-helix	337-356	20
β-strand	359-360	2	3
α-helix	366-368	3
β-strand	369-371	3	2
α-helix	373-375	3
β-strand	377-379	3	2
β-strand	385-386	2	3
β-strand	393-394	2	4
α-helix	395-396	2
α-helix	403-405	3
α-helix	408-413	6
β-strand	415-416	2	4
α-helix	418-433	16
α-helix	437-438	2
α-helix	445-447	3
α-helix	448-453	6
α-helix	458-461	4
α-helix	466-475	10
α-helix	480-482	3
α-helix	484-485	2
α-helix	486-501	16

Chain B: 21 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	236	1	5
α-helix	239-241	3
β-strand	242-247	6	5
α-helix	248-251	4
β-strand	256-261	6	5
β-strand	266-271	6	5
α-helix	280-292	13
β-strand	298	1	6
α-helix	299-300	2
β-strand	301-305	5	5
α-helix	311	1
β-strand	312-316	5	5
β-strand	322	1	6
α-helix	323-329	7
α-helix	337-356	20
β-strand	359-360	2	7
α-helix	366-368	3
β-strand	369-371	3	6
α-helix	373-375	3
β-strand	377-379	3	6
β-strand	385-386	2	7
β-strand	393-394	2	8
α-helix	395-396	2
α-helix	403-405	3
α-helix	408-413	6
β-strand	415-416	2	8
α-helix	418-433	16
α-helix	437-438	2
α-helix	445-447	3
α-helix	448-453	6
α-helix	458-461	4
α-helix	466-475	10
α-helix	480-482	3
α-helix	484-485	2
α-helix	486-499	14

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>3DK3_1 Proto-oncogene tyrosine-protein kinase ABL1 (chains A, B)
MSLDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAV
MKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVSAVVLLYMATQISS
AMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTFTAHAGAKFPIKWTAPE
SLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDPSQVYELLEKDYRMERPEGCPEKVY
ELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKELGKRGEGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
SX7	2-amino-5-[3-(1-ethyl-1H-pyrazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N,N-dimet…	C21 H22 N6 O	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Crystal structure of mutant ABL kinase domain in complex with small molecule fragment. Bounaud, P.-Y., Gosberg, A., Hendle, J. et al. To be published.

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

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