2HYY: Human Abl kinase domain

Human Abl kinase domain in complex with imatinib (STI571, Glivec). Determined by X-ray diffraction at 2.4 Å resolution. Released 16 Jan 2007.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,702
Mol. weight: 128.69 kDa
Ligands: STI
Released: 16 Jan 2007

Explore 2HYY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2HYY contains 81 α-helices and 48 β-strands across 4 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	236	1	1
β-strand	242-247	6	1
α-helix	248-251	4
β-strand	256-261	6	1
α-helix	262-264	3
β-strand	266-272	7	1
α-helix	280-291	12
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	321-322	2	2
α-helix	323-329	7
α-helix	337-356	20
α-helix	366-368	3
β-strand	369-371	3	2
α-helix	373-375	3
β-strand	377-379	3	2
α-helix	384-387	4
β-strand	394-396	3	3
β-strand	399-401	3	3
α-helix	403-405	3
α-helix	408-413	6
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	486-496	11

Chain B: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	236	1	4
α-helix	239-241	3
β-strand	242-247	6	4
α-helix	248-251	4
β-strand	256-261	6	4
α-helix	262-264	3
β-strand	266-272	7	4
α-helix	280-291	12
β-strand	298	1	5
β-strand	301-305	5	4
α-helix	311	1
β-strand	312-316	5	4
β-strand	322	1	5
α-helix	323-329	7
α-helix	337-356	20
α-helix	366-368	3
β-strand	369-372	4	5
α-helix	373-375	3
β-strand	376-379	4	5
α-helix	384-387	4
β-strand	394-396	3	6
β-strand	399-401	3	6
α-helix	403-405	3
α-helix	408-413	6
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	486-497	12

Chain C: 20 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	236	1	7
α-helix	239-241	3
β-strand	242-247	6	7
α-helix	249-251	3
β-strand	256-261	6	7
α-helix	262-264	3
β-strand	266-273	8	7
α-helix	280-291	12
β-strand	298	1	8
α-helix	299-300	2
β-strand	301-305	5	7
β-strand	311-316	6	7
β-strand	322	1	8
α-helix	323-329	7
α-helix	337-356	20
α-helix	366-368	3
β-strand	369-371	3	8
α-helix	373-375	3
β-strand	377-379	3	8
α-helix	384-387	4
β-strand	394-396	3	9
β-strand	399-401	3	9
α-helix	403-405	3
α-helix	408-413	6
α-helix	418-433	16
α-helix	437-438	2
α-helix	445-453	9
α-helix	458-461	4
α-helix	466-475	10
α-helix	480-482	3
α-helix	484-485	2
α-helix	486-497	12

Chain D: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	236	1	10
α-helix	239-241	3
β-strand	242-247	6	10
α-helix	248-251	4
β-strand	256-261	6	10
β-strand	266-271	6	10
α-helix	280-292	13
β-strand	298	1	11
β-strand	301-305	5	10
α-helix	311	1
β-strand	312-316	5	10
β-strand	321-322	2	11
α-helix	323-329	7
α-helix	337-356	20
α-helix	366-368	3
β-strand	369-371	3	11
α-helix	373-375	3
β-strand	377-379	3	11
α-helix	384-387	4
β-strand	394-396	3	12
β-strand	399-401	3	12
α-helix	408-413	6
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	486-497	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proto-oncogene tyrosine-protein kinase ABL1	A, B, C, D	protein	273	Homo sapiens	P00519 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>2HYY_1 Proto-oncogene tyrosine-protein kinase ABL1 (chains A, B, C, D)
VSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEA
AVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQI
SSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTA
PESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEK
VYELMRACWQWNPSDRPSFAEIHQAFETMFQES

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	4

Primary citation

Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia. Cowan-Jacob, S.W., Fendrich, G., Floersheimer, A. et al. Acta Crystallogr D Biol Crystallogr (2007) 63:80-93. DOI 10.1107/S0907444906047287 · PubMed

Other PDB entries of the same protein (UniProt P00519 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5OAZ 1.03 Å, Crystal structure of the Abl-SH3 domain at pH 7.5
7PVS 1.05 Å, Crystal structure of the Abl SH3 domain V73E-A74S-S75R-G76T-D77E-G92N-Y93N-N94T-H95E…
4J9C 1.05 Å, Crystal structure of the Abl-SH3 domain H59Q-N96T mutant complexed with the designed…
4J9F 1.09 Å, Crystal structure of the Abl-SH3 domain complexed with the high affinity peptide P0
7PW2 1.1 Å, Crystal structure of the Abl SH3 domain V73E-A74S-S75R-G76T-D77E mutant
3EG3 1.4 Å, Crystal structure of the N114A mutant of ABL-SH3 domain
4J9E 1.4 Å, Crystal structure of the N114A mutant of the Abl-SH3 domain complexed with the high…
5DC4 1.48 Å, Crystal structure of monobody AS25/ABL1 SH2 domain complex, crystal a
4J9D 1.5 Å, Crystal structure of the N114A mutant of the Abl-SH3 domain complexed with the high…
5HU9 1.53 Å, Crystal structure of ABL1 in complex with CHMFL-074
7PVQ 1.55 Å, Crystal structure of the Abl SH3 domain V73E-A74S-S75R-G76T-D77E-G92N-Y93N-N94T-H95E…
5DC9 1.56 Å, Crystal structure of monobody AS25/ABL1 SH2 domain complex, crystal B

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2HYY is part of these collections:

Kinases and cancer drug targets

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