4U0I: KIT

Crystal structure of KIT in complex with ponatinib. Determined by X-ray diffraction at 2.0 Å resolution. Released 8 Oct 2014.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,546
Mol. weight: 36.34 kDa
Ligands: 0LI, PO4
Released: 8 Oct 2014

Explore 4U0I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4U0I contains 20 α-helices and 14 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: 20 helices, 14 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
β-strand	677	1	2
α-helix	678-685	8
α-helix	686-688	3
β-strand	690	1	3
β-strand	765	1	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	812-814	3
β-strand	824-825	2	4
β-strand	830-831	2	4
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	917-930	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mast/stem cell growth factor receptor Kit,Mast/stem cell growth factor receptor Kit	A	protein	315	Homo sapiens	P10721 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4U0I_1 Mast/stem cell growth factor receptor Kit,Mast/stem cell growth factor receptor Kit (chains A)
INGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAMTVAV
KMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFL
RRKRDSFICSKTSPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILL
THGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLW
ELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQI
VQLIEKQISESTNHI

Ligands and cofactors

ID	Name	Formula	Copies
0LI	3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)…	C29 H27 F3 N6 O	1
PO4	Phosphate ion	O4 P	2

Primary citation

Ponatinib Inhibits Polyclonal Drug-Resistant KIT Oncoproteins and Shows Therapeutic Potential in Heavily Pretreated Gastrointestinal Stromal Tumor (GIST) Patients. Garner, A.P., Gozgit, J.M., Anjum, R. et al. Clin Cancer Res (2014) 20:5745-5755. DOI 10.1158/1078-0432.CCR-14-1397 · 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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