8S16: C-KIT kinase domain

c-KIT kinase domain in complex with imatinib. Determined by X-ray diffraction at 1.85 Å resolution. Released 3 Sept 2025.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,213
Mol. weight: 75.48 kDa
Ligands: STI
Released: 3 Sept 2025

Explore 8S16 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8S16 contains 42 α-helices and 30 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: 23 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	573-575	3
α-helix	580-582	3
β-strand	583	1	1
α-helix	586-588	3
β-strand	589-597	9	1
β-strand	601-608	8	1
β-strand	612	1	2
β-strand	618-625	8	1
α-helix	631-647	17
β-strand	653	1	3
α-helix	654-655	2
β-strand	656-660	5	1
β-strand	667-671	5	1
β-strand	677	1	3
α-helix	678-685	8
α-helix	686-688	3
β-strand	690	1	4
α-helix	759-761	3
β-strand	765	1	4
α-helix	766-785	20
α-helix	795-797	3
β-strand	798-801	4	3
α-helix	802-804	3
β-strand	805-808	4	3
α-helix	812-814	3
α-helix	817-819	3
β-strand	824-826	3	5
β-strand	829-831	3	5
α-helix	833-835	3
α-helix	838-843	6
α-helix	848-863	16
α-helix	867-868	2
α-helix	877-885	9
α-helix	889-892	4
α-helix	897-906	10
α-helix	911-913	3
α-helix	915-916	2
α-helix	917-931	15

Chain B: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	580-582	3
β-strand	583	1	6
α-helix	586-588	3
β-strand	589-597	9	6
β-strand	601-609	9	6
β-strand	612	1	2
β-strand	617-625	9	6
α-helix	631-647	17
β-strand	653	1	7
α-helix	654-655	2
β-strand	656-660	5	6
β-strand	667-671	5	6
β-strand	677	1	7
α-helix	678-685	8
α-helix	686-688	3
β-strand	690	1	8
β-strand	765	1	8
α-helix	766-785	20
α-helix	795-797	3
β-strand	798-800	3	7
β-strand	806-808	3	7
α-helix	812-814	3
β-strand	824-826	3	9
β-strand	829-831	3	9
α-helix	833-835	3
α-helix	838-843	6
α-helix	848-863	16
α-helix	867-868	2
α-helix	877-884	8
α-helix	889-892	4
α-helix	897-906	10
α-helix	911-913	3
α-helix	915-916	2
α-helix	917-930	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mast/stem cell growth factor receptor Kit	A, B	protein	327	Homo sapiens	P10721 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8S16_1 Mast/stem cell growth factor receptor Kit (chains A, B)
GSMPMYEVQWKVVEESNGNNYSYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEAT
AQGLIKSDAAMTVAVKMLKPSAHSTEREALMSELKVLSYLGNHENIVNLLGACTHGGPTL
VITEYCCYGDLLNFLRRKRDEFVPYKVAPEDLYKDFLTLEHLLSFSYQVAKGMAFLASKN
CIHRDLAARNILLTHGNITKICDFGLARDIKNDSNYVDKGNARLPVKWMAPESIFNSVYT
FESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMSSPEYAPAEMYDIMKTCW
DADPDKRPTFKQIVQDIEKQISESTNH

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

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

Primary citation

c-KIT kinase domain in complex with imatinib. Teuber, A., Niggenaber, J., Kleinboelting, S.B. et al. To be published.

Other PDB entries of the same protein (UniProt P10721 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VIF 1.45 Å, Crystal structure of SOCS6 SH2 domain in complex with a c-KIT phosphopeptide
8PQD 1.5 Å, c-KIT kinase domain in complex with avapritinib derivative 10
8S14 1.5 Å, c-KIT kinase domain in complex with sunitinib
1T46 1.6 Å, Structural basis for the autoinhibition and sti-571 inhibition of C-kit tyrosine kinase
3G0E 1.6 Å, KIT kinase domain in complex with sunitinib
8PQA 1.65 Å, c-KIT kinase domain in complex with avapritinib derivative 4
9TFD 1.65 Å, KIT kinase domain in complex with a pyrrolotriazine-based compound (11)
8PQ9 1.7 Å, c-KIT kinase domain in complex with avapritinib
9TFE 1.7 Å, KIT kinase domain in complex with an aminopyrimidine-based compound (15)
9TFG 1.7 Å, KIT kinase domain in complex with a 6-,7-dimethoxyquinoline-based compound (19)
9TFH 1.7 Å, KIT kinase domain in complex with a 7-methylquinazoline-based compound (25)
9TFK 1.7 Å, KIT kinase domain in complex with a quinoline-3-carbonitrile-based compound (38)

Browse structure collections

About this viewer

MolViewer shows 8S16 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.