MolNFT v1 · #127484 · protein

Crystal structure of human sr protein kinase 1 (SRPK1) in complex with compound 1

5MXX: “Crystal structure of human sr protein kinase 1 (SRPK1) in complex with compound 1”. X-ray diffraction, 2 ligands (W4A, CA), 3 pockets (best druggability 0.72). MolNFT v1 #127484 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5MXX
Type: protein
Length: 361 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SRPK1
Ligands: W4A, CA
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SRPK1	protein	361	44% helix, 16% strand	—

Ligands and binding sites

W4A · 5-methyl-~{N}-[2-(4-methylpiperazin-1-yl)-5-(trifluoromethyl)phenyl]furan-2-carboxamide · ligand · chains A
CA · Calcium ion · metal · 4 copies · chains A
EDO · 1,2-ethanediol · additive · 12 copies · chains A
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	492	0.72	0.81	44	W4A, EDO
2	125	0.44	0.77	20	EDO
3	63	0.32	0.75	12	EDO

Compared structures

5MXX · Crystal structure of human SR protein kinase 1 (SRPK1) in complex with compound 1 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5MXX · PDBe 5MXX

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