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Human PRPF4B bound to benzothiophene inhibitor 224

Analyse Human PRPF4B bound to benzothiophene inhibitor 224 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PJJ
Type: protein
Length: 1,290 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase PRP4 homolog
EC: 2.7.11.1
UniProt: Q13523
Ligands: OCJ, PO4
Pockets: 12 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase PRP4 homolog (EC 2.7.11.1)	protein	321	40% helix, 18% strand	Q13523
B	SERINE/THREONINE-protein kinase PRP4 homolog (EC 2.7.11.1)	protein	326	40% helix, 19% strand	Q13523
C	SERINE/THREONINE-protein kinase PRP4 homolog (EC 2.7.11.1)	protein	326	40% helix, 19% strand	Q13523
D	SERINE/THREONINE-protein kinase PRP4 homolog (EC 2.7.11.1)	protein	317	41% helix, 18% strand	Q13523

Ligands and binding sites

OCJ · 4-(5-{[(3-aminophenyl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide · ligand · 4 copies · chains A, B, D, C
PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D

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

Pockets

12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1097	0.73	0.76	110	EDO
2	572	0.72	0.80	52	OCJ
3	272	0.62	0.80	31	OCJ
4	179	0.61	0.83	28	OCJ
5	241	0.60	0.80	38	PO4

Interfaces

5 interfaces between chains.

B–D · 686 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 647 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 343 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 74 Å² buried · 1 hydrogen bond · protein-protein
A–D · 32 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

6PJJ · Human PRPF4B bound to benzothiophene inhibitor 224 · the same entry in another collection · chain D against D, TM-score 1.00
Q13523 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase PRP4 homolog… · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q13523
Elsewhere: RCSB PDB 6PJJ · PDBe 6PJJ · UniProt Q13523

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