7NG7: Src kinase

Src kinase bound to eCF506 trapped in inactive conformation. Determined by X-ray diffraction at 1.5 Å resolution. Released 15 Sept 2021.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,477
Mol. weight: 33.33 kDa
Ligands: UCW
Released: 15 Sept 2021

Explore 7NG7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NG7 contains 22 α-helices and 10 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, 10 β-strands

Element	Residues	Length	Sheet
β-strand	264	1	1
α-helix	267-269	3
β-strand	270-278	9	1
β-strand	283-289	7	1
β-strand	293-299	7	1
α-helix	307-318	12
β-strand	325	1	2
α-helix	326-327	2
β-strand	328-332	5	1
α-helix	337	1
β-strand	338-341	4	1
β-strand	348	1	2
α-helix	349-354	6
α-helix	358-360	3
α-helix	363-382	20
α-helix	392-394	3
β-strand	395-397	3	2
α-helix	399-401	3
β-strand	403-405	3	2
α-helix	410-412	3
α-helix	420-422	3
α-helix	429-431	3
α-helix	434-439	6
α-helix	444-459	16
α-helix	463-464	2
α-helix	471-479	9
α-helix	486-487	2
α-helix	492-501	10
α-helix	506-508	3
α-helix	510-511	2
α-helix	512-520	9
α-helix	522-525	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proto-oncogene tyrosine-protein kinase Src	A	protein	287	Homo sapiens	P12931 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7NG7_1 Proto-oncogene tyrosine-protein kinase Src (chains A)
GSDIQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEA
FLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKGETGKYLRLPQLVDM
AAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLIEDNEYTARQGAKFPI
KWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPE
CPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFTSTEPQYQPGENL

Ligands and cofactors

ID	Name	Formula	Copies
UCW	tert-butyl (4-(4-amino-1-(2-(4-(dimethylamino)piperidin-1-yl)ethyl)-1H-pyrazolo…	C26 H38 N8 O3	1

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

Primary citation

A Conformation Selective Mode of Inhibiting SRC Improves Drug Efficacy and Tolerability. Temps, C., Lietha, D., Webb, E.R. et al. Cancer Res (2021) 81:5438-5450. DOI 10.1158/0008-5472.CAN-21-0613 · PubMed

Other PDB entries of the same protein (UniProt P12931 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9OFX 1.45 Å, Crystal structure of c-Src SH3 domain in H32 space group mediated by nickel
1FMK 1.5 Å, Crystal structure of human tyrosine-protein kinase C-src
1O43 1.5 Å, Crystal structure of SH2 in complex with RU82129.
1O4A 1.5 Å, Crystal structure of SH2 in complex with RU82197.
1O4R 1.5 Å, Crystal structure of SH2 in complex with RU78783.
2SRC 1.5 Å, Crystal structure of human tyrosine-protein kinase C-src, in complex with AMP-pnp
6C4S 1.5 Å, Human cSrc SH3 Domain in complex with Choline Kinase fragment 60-69
8VCF 1.5 Å, Crystal structure of Superbinder Src SH2 domain with Cysteine to Serine mutations
1O48 1.55 Å, Crystal structure of SH2 in complex with RU85053.
1O4G 1.55 Å, Crystal structure of SH2 in complex with DPI59.
1O4K 1.57 Å, Crystal structure of SH2 in complex with pasbn.
4F5B 1.57 Å, Triple mutant Src SH2 domain bound to phosphotyrosine

Browse structure collections

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