6ITV: Activated c-KIT

Crystal structure of activated c-KIT in complex with compound. Determined by X-ray diffraction at 1.88 Å resolution. Released 27 Nov 2019.

Method: X-ray diffraction
Resolution: 1.88 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,646
Mol. weight: 38.27 kDa
Ligands: AWO
Released: 27 Nov 2019

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

Secondary structure: helices and β-sheets

6ITV contains 22 α-helices and 12 β-strands across 1 chain. 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, 12 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	601-609	9	1
β-strand	617-625	9	1
α-helix	631-647	17
β-strand	653	1	2
α-helix	654-655	2
β-strand	656-660	5	1
β-strand	667-671	5	1
α-helix	672-673	2
β-strand	677	1	2
α-helix	678-686	9
α-helix	759-785	27
α-helix	795-797	3
β-strand	798-801	4	2
α-helix	802-804	3
β-strand	805-808	4	2
α-helix	812-814	3
α-helix	817-819	3
β-strand	824-826	3	3
β-strand	829-831	3	3
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mast/stem cell growth factor receptor Kit	A	protein	331	Homo sapiens	P10721 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6ITV_1 Mast/stem cell growth factor receptor Kit (chains A)
YLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEA
TAYGLIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPT
LVITEYCCYGDLLNFLRRKRDSFICSKTSPAIMEDDELALDLEDLLSFSYQVAKGMAFLA
SKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNC
VYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMK
TCWDADPLKRPTFKQIVQLIEKQISESTNHI

Ligands and cofactors

ID	Name	Formula	Copies
AWO	N-(5-ethyl-1,2-oxazol-3-yl)-N'-[4-(2-{[6-(4-ethylpyrazin-1(4H)-yl)pyrimidin-4-y…	C25 H25 N9 O2 S	1

Primary citation

Crystal structure of activated c-KIT in complex with compound. Wu, T.S., Wu, S.Y. 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)

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