3ZH8: A novel small molecule aPKC inhibitor

A novel small molecule aPKC inhibitor. Determined by X-ray diffraction at 2.74 Å resolution. Released 27 Feb 2013.

Method: X-ray diffraction
Resolution: 2.74 Å
Organism: HOMO SAPIENS
Chains: 3
Atoms: 7,714
Mol. weight: 124.45 kDa
Ligands: C58
Released: 27 Feb 2013

Explore 3ZH8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3ZH8 contains 57 α-helices and 43 β-strands across 3 chains. 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: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	242-244	3
β-strand	245-253	9	1
β-strand	257-264	8	1
β-strand	269-277	9	1
α-helix	278-284	7
α-helix	289-301	13
β-strand	306	1	2
α-helix	307-308	2
β-strand	309-314	6	1
β-strand	318-324	7	1
β-strand	330	1	2
α-helix	331-338	8
α-helix	343-362	20
β-strand	366	1	3
α-helix	372-374	3
β-strand	375-377	3	2
β-strand	383-385	3	2
β-strand	392	1	3
β-strand	401	1	4
α-helix	408-410	3
α-helix	413-416	4
β-strand	421	1	4
α-helix	424-439	16
α-helix	457-467	11
α-helix	469-470	2
α-helix	478-487	10
α-helix	503-509	7
α-helix	511-513	3
α-helix	518-522	5
β-strand	535	1	5
α-helix	554-557	4
α-helix	559-562	4
α-helix	568-570	3
β-strand	575-576	2	1

Chains B and C: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	242-244	3
β-strand	245-253	9	5
β-strand	257-264	8	5
β-strand	269-277	9	5
α-helix	278-284	7
α-helix	289-301	13
β-strand	306	1	6
α-helix	307-308	2
β-strand	309-314	6	5
β-strand	318-324	7	5
β-strand	330	1	6
α-helix	331-338	8
α-helix	343-362	20
β-strand	366	1	7
α-helix	372-374	3
β-strand	375-377	3	6
β-strand	383-385	3	6
β-strand	392	1	7
β-strand	401	1	8
α-helix	408-410	3
α-helix	413-416	4
β-strand	421	1	8
α-helix	424-439	16
α-helix	457-467	11
α-helix	469-470	2
α-helix	478-487	10
α-helix	503-509	7
α-helix	511-513	3
α-helix	518-522	5
α-helix	554-557	4
α-helix	559-562	4
α-helix	568-570	3
β-strand	575-576	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein kinase C iota type	A, B, C	protein	349	HOMO SAPIENS	P41743 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>3ZH8_1 PROTEIN KINASE C IOTA TYPE (chains A, B, C)
SLGLQDFDLLRVIGRGSYAKVLLVRLKKTDRIYAMKVVKKELVNDDEDIDWVQTEKHVFE
QASNHPFLVGLHSCFQTESRLFFVIEYVNGGDLMFHMQRQRKLPEEHARFYSAEISLALN
YLHERGIIYRDLKLDNVLLDSEGHIKLTDYGMCKEGLRPGDTTSTFCGTPNYIAPEILRG
EDYGFSVDWWALGVLMFEMMAGRSPFDIVGSSDNPDQNTEDYLFQVILEKQIRIPRSLSV
KAASVLKSFLNKDPKERLGCHPQTGFADIQGHPFFRNVDWDMMEQKQVVPPFKPNISGEF
GLDNFDSQFTNEPVQLTPDDDDIVRKIDQSEFEGFEYINPLLMSAEESV

Ligands and cofactors

ID	Name	Formula	Copies
C58	(2S)-3-phenyl-N~1~-[2-(pyridin-4-yl)-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyr…	C24 H25 N5 S	3

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

Primary citation

Adenosine-Binding Motif Mimicry and Cellular Effects of a Thieno[2,3-D]Pyrimidine-Based Chemical Inhibitor of Atypical Protein Kinase C Isozymes. Kjaer, S., Linch, M., Purkiss, A. et al. Biochem J (2013) 451:329. DOI 10.1042/BJ20121871 · PubMed

Other PDB entries of the same protein (UniProt P41743 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1WMH 1.5 Å, Crystal structure of a PB1 domain complex of Protein kinase c iota and Par6 alpha
5LI9 1.79 Å, Structure of a nucleotide-bound form of PKCiota core kinase domain
3A8X 2.0 Å, Crystal Structure of PKCiota kinase domain
5LI1 2.0 Å, Structure of a Par3-inhibitory peptide bound to PKCiota core kinase domain
3A8W 2.1 Å, Crystal Structure of PKCiota kinase domain
8R3X 2.59 Å, Crystal structure of aPKC Iota kinase domain with LLGL2 peptide
1ZRZ 3.0 Å, Crystal Structure of the Catalytic Domain of Atypical Protein Kinase C-iota
9EJK 3.08 Å, Lgl2 bound to the aPKCiota-Par6b complex in nucleotide-free form. Head sub-complex…
5LIH 3.25 Å, Structure of a peptide-substrate bound to PKCiota core kinase domain
6ILZ 3.26 Å, Crystal structure of PKCiota in complex with inhibitor
9EJM 3.33 Å, Lgl2 bound to the aPKCiota-Par6B complex in its ADP-bound form
9EJL 3.48 Å, Lgl2 bound to the aPKCiota-Par6B complex in nucleotide-free form. Conformation with…

Browse structure collections

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