6MOB: KIT1

Crystal structure of KIT1 in complex with DP2976 via co-crystallization. Determined by X-ray diffraction at 1.8 Å resolution. Released 31 Jul 2019.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,888
Mol. weight: 36.67 kDa
Ligands: JWY
Released: 31 Jul 2019

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

Secondary structure: helices and β-sheets

6MOB contains 21 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: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	570-572	3
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
β-strand	676-677	2	2
α-helix	678-683	6
α-helix	686-688	3
α-helix	766-785	20
α-helix	795-797	3
β-strand	798-801	4	2
β-strand	805-808	4	2
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	917-928	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mast/stem cell growth factor receptor Kit	A	protein	312	Homo sapiens	P10721 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6MOB_1 Mast/stem cell growth factor receptor Kit (chains A)
NNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAMTVAVKML
KPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRK
RDSFICSKTSPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHG
RITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELF
SLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQL
IEKQISESTNHI

Ligands and cofactors

ID	Name	Formula	Copies
JWY	N-{4-chloro-5-[1-ethyl-7-(methylamino)-2-oxo-1,2-dihydro-1,6-naphthyridin-3-yl]…	C24 H21 Cl F N5 O2	1

Water and common crystallization additives (NO3) are not listed.

Primary citation

Ripretinib (DCC-2618) Is a Switch Control Kinase Inhibitor of a Broad Spectrum of Oncogenic and Drug-Resistant KIT and PDGFRA Variants. Smith, B.D., Kaufman, M.D., Lu, W.P. et al. Cancer Cell (2019) 35:738-751.e9. DOI 10.1016/j.ccell.2019.04.006 · PubMed

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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