7ZKS: SRPK1

SRPK1 in complex with inhibitor. Determined by X-ray diffraction at 2.28 Å resolution. Released 22 Feb 2023.

Method: X-ray diffraction
Resolution: 2.28 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,030
Mol. weight: 44.58 kDa
Ligands: IXQ
Released: 22 Feb 2023

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

Secondary structure: helices and β-sheets

7ZKS contains 21 α-helices and 15 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, 15 β-strands

Element	Residues	Length	Sheet
β-strand	75-76	2	1
β-strand	80-88	9	1
β-strand	92-99	8	1
β-strand	104-111	8	1
α-helix	115-133	19
α-helix	139-143	5
β-strand	144	1	2
β-strand	149-155	7	1
β-strand	158-166	9	1
β-strand	170-171	2	2
α-helix	172-178	7
α-helix	186-202	17
α-helix	203-207	5
β-strand	209-210	2	3
α-helix	216-218	3
β-strand	219-221	3	2
α-helix	225-236	12
α-helix	485-490	6
β-strand	493-495	3	2
α-helix	498-500	3
β-strand	502-503	2	3
β-strand	506	1	3
α-helix	515-517	3
α-helix	520-524	5
α-helix	531-546	16
α-helix	561-573	13
α-helix	576-577	2
α-helix	578-583	6
α-helix	587-590	4
β-strand	591	1	4
β-strand	597	1	4
α-helix	608-614	7
α-helix	620-630	11
α-helix	631-634	4
α-helix	642-643	2
α-helix	644-648	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SRSF protein kinase 1	A	protein	387	Homo sapiens	Q96SB4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7ZKS_1 SRSF protein kinase 1 (chains A)
GSDDDEQEDPNDYCKGGYHLVKIGDLFNGRYHVIRKLGWGHFSTVWLSWDIQGKKFVAMK
VVKSAEHYTETALDEIRLLKSVRNSDPNDPNREMVVQLLDDFKISGVNGTHICMVFEVLG
HHLLKWIIKSNYQGLPLPCVKKIIQQVLQGLDYLHTKCRIIHTDIKPENILLSVNEQYIR
RLAAEATEWQRSGAPPPSGSAVSTAPAGNFLVNPLEPKNAEKLKVKIADLGNACWVHKHF
TEDIQTRQYRSLEVLIGSGYNTPADIWSTACMAFELATGDYLFEPHSGEEYTRDEDHIAL
IIELLGKVPRKLIVAGKYSKEFFTKKGDLKHITKLKPWGLFEVLVEKYEWSQEEAAGFTD
FLLPMLELIPEKRATAAECLRHPWLNS

Ligands and cofactors

ID	Name	Formula	Copies
IXQ	N-[3-[[[2-(6-chloranyl-5-fluoranyl-1H-benzimidazol-2-yl)pyrimidin-4-yl]amino]me…	C19 H17 Cl F N7 O2 S	1

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

Primary citation

MSC-1186, a Highly Selective Pan-SRPK Inhibitor Based on an Exceptionally Decorated Benzimidazole-Pyrimidine Core. Schroder, M., Leiendecker, M., Gradler, U. et al. J Med Chem (2023) 66:837-854. DOI 10.1021/acs.jmedchem.2c01705 · PubMed

Other PDB entries of the same protein (UniProt Q96SB4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NNG 1.2 Å, Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated…
5MY8 1.7 Å, Crystal structure of SRPK1 in complex with SPHINX31
1WAK 1.73 Å, X-ray structure of SRPK1
5MXX 1.75 Å, Crystal structure of human SR protein kinase 1 (SRPK1) in complex with compound 1
4WUA 2.0 Å, Crystal structure of human SRPK1 complexed to an inhibitor SRPIN340
7DD1 2.05 Å, Crystal structure of SRPK1 in complex with a peptide inhibitor
7PQS 2.2 Å, SRPK1 in complex with MSC2711186
5XV7 2.32 Å, SRPK1 in complex with Alectinib
1WBP 2.4 Å, SRPK1 bound to 9mer docking motif peptide
6FAD 2.8 Å, SR protein kinase 1 (SRPK1) in complex with the RGG-box of HSV1 ICP27
3BEG 2.9 Å, Crystal structure of SR protein kinase 1 complexed to its substrate ASF/SF2

Browse structure collections

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