3G0E: KIT kinase domain

KIT kinase domain in complex with sunitinib. Determined by X-ray diffraction at 1.6 Å resolution. Released 24 Feb 2009.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,022
Mol. weight: 38.62 kDa
Ligands: B49
Released: 24 Feb 2009

Explore 3G0E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3G0E contains 21 α-helices and 18 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, 18 β-strands

Element	Residues	Length	Sheet
α-helix	549-551	3
β-strand	558-559	2	1
β-strand	560-564	5	2
β-strand	567-570	4	2
α-helix	573-575	3
α-helix	580-582	3
β-strand	583	1	3
α-helix	586-588	3
β-strand	589-597	9	3
β-strand	601-609	9	3
β-strand	617-625	9	3
α-helix	631-647	17
β-strand	653	1	4
β-strand	656-660	5	3
β-strand	667-671	5	3
β-strand	677	1	4
α-helix	678-685	8
α-helix	686-689	4
α-helix	753-756	4
β-strand	757	1	5
β-strand	760	1	5
α-helix	766-785	20
β-strand	788-789	2	1
α-helix	795-797	3
β-strand	798-801	4	4
β-strand	805-808	4	4
α-helix	812-814	3
α-helix	817-819	3
β-strand	824-826	3	6
β-strand	829-831	3	6
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	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	A	protein	336	Homo sapiens	P10721 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3G0E_1 Mast/stem cell growth factor receptor (chains A)
GPTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFG
KVVEATAYGLIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACT
IGGPTLVITEYCCYGDLLNFLRRKRDSFICSKTSPAIMEDDELALDLEDLLSFSYQVAKG
MAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPE
SIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEM
YDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHI

Ligands and cofactors

ID	Name	Formula	Copies
B49	N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene…	C22 H27 F N4 O2	1

Primary citation

KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients. Gajiwala, K.S., Wu, J.C., Christensen, J. et al. Proc Natl Acad Sci U S A (2009) 106:1542-1547. DOI 10.1073/pnas.0812413106 · 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
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)
9TFJ 1.75 Å, KIT kinase domain in complex with a 6,7-dimethoxyquinazoline-based compound (34)

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