5MY8: SRPK1

Crystal structure of SRPK1 in complex with SPHINX31. Determined by X-ray diffraction at 1.7 Å resolution. Released 10 May 2017.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,511
Mol. weight: 45.71 kDa
Ligands: RXZ, CIT
Released: 10 May 2017

Explore 5MY8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MY8 contains 23 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: 23 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	147-154	8	1
β-strand	159-166	8	1
β-strand	171	1	2
α-helix	172-178	7
α-helix	186-201	16
α-helix	202-207	6
β-strand	209-210	2	3
α-helix	216-218	3
β-strand	219-221	3	2
α-helix	222-224	3
α-helix	225-238	14
α-helix	485-490	6
β-strand	493-495	3	2
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	587-589	3
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	638-640	3
α-helix	642-643	2
α-helix	644-648	5
α-helix	651-654	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SRSF protein kinase 1,SRSF protein kinase 1	A	protein	383	Homo sapiens	Q96SB4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5MY8_1 SRSF protein kinase 1,SRSF protein kinase 1 (chains A)
SMDPNDYCKGGYHLVKIGDLFNGRYHVIRKLGWGHFSTVWLSWDIQGKKFVAMKVVKSAE
HYTETALDEIRLLKSVRNSDPNDPNREMVVQLLDDFKISGVNGTHICMVFEVLGHHLLKW
IIKSNYQGLPLPCVKKIIQQVLQGLDYLHTKCRIIHTDIKPENILLSVNEQYIRRLAAEA
TEWQRSGAPPPSGSAVSTAPATAGNFLVNPLEPKNAEKLKVKIADLGNACWVHKHFTEDI
QTRQYRSLEVLIGSGYNTPADIWSTACMAFELATGDYLFEPHSGEEYTRDEDHIALIIEL
LGKVPRKLIVAGKYSKEFFTKKGDLKHITKLKPWGLFEVLVEKYEWSQEEAAGFTDFLLP
MLELIPEKRATAAECLRHPWLNS

Ligands and cofactors

ID	Name	Formula	Copies
RXZ	SPHINX31	C27 H24 F3 N5 O2	1
CIT	Citric acid	C6 H8 O7	1

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

Primary citation

Development of Potent, Selective SRPK1 Inhibitors as Potential Topical Therapeutics for Neovascular Eye Disease. Batson, J., Toop, H.D., Redondo, C. et al. ACS Chem Biol (2017) 12:825-832. DOI 10.1021/acschembio.6b01048 · 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…
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
7ZKS 2.28 Å, SRPK1 in complex with inhibitor
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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