4HVS: Mast/stem cell growth factor receptor Kit

Crystal structure of KIT kinase domain with a small molecule inhibitor, PLX647. Determined by X-ray diffraction at 1.9 Å resolution. Released 27 Mar 2013.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,728
Mol. weight: 38.42 kDa
Ligands: 647
Released: 27 Mar 2013

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

Secondary structure: helices and β-sheets

4HVS contains 23 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: 23 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	550-552	3
β-strand	558-559	2	1
β-strand	560-562	3	2
β-strand	568-570	3	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	686-688	3
β-strand	689-690	2	5
α-helix	691	1
α-helix	754-756	3
α-helix	760-762	3
β-strand	764-765	2	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	824-825	2	6
β-strand	830-831	2	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	917-929	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mast/stem cell growth factor receptor Kit	A	protein	335	Homo sapiens	P10721 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4HVS_1 Mast/stem cell growth factor receptor Kit (chains A)
MGHHHHHHMPMYEVQWKVVEESNGNNYSYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFG
KVVEATAQGLIKSDAAMTVAVKMLKPSAHSTEREALMSELKVLSYLGNHENIVNLLGACT
HGGPTLVITEYCCYGDLLNFLRRKRDSFHSSDTSPASMEDDENALDLEDLLSFSYQVAKG
MAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVDKGNARLPVKWMAPE
SIFNSVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMSSPEHAPAEM
YDIMKTCWDADPDKRPTFKQIVQDIEKQISESTNH

Ligands and cofactors

ID	Name	Formula	Copies
647	5-(1H-pyrrolo[2,3-b]pyridin-3-ylmethyl)-N-[4-(trifluoromethyl)benzyl]pyridin-2-…	C21 H17 F3 N4	1

Primary citation

Design and pharmacology of a highly specific dual FMS and KIT kinase inhibitor. Zhang, C., Ibrahim, P.N., Zhang, J. et al. Proc Natl Acad Sci U S A (2013) 110:5689-5694. DOI 10.1073/pnas.1219457110 · 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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