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Crystal structure of human CLK1 in complex with PYRIDO[3,4- G]QUINAZOLINE derivative ZW29 (compound 13)

Analyse Crystal structure of human CLK1 in complex with PYRIDO[3,4- G]QUINAZOLINE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5J1V
Type: protein
Length: 989 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dual specificity protein kinase CLK1
EC: 2.7.12.1
UniProt: P49759
Ligands: 6FD
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dual specificity protein kinase CLK1 (EC 2.7.12.1)	protein	338	40% helix, 20% strand	P49759
B	Dual specificity protein kinase CLK1 (EC 2.7.12.1)	protein	337	40% helix, 20% strand	P49759
C	Dual specificity protein kinase CLK1 (EC 2.7.12.1)	protein	314	38% helix, 21% strand	P49759

Ligands and binding sites

6FD · pyrido[3,4-g]quinazoline-2,10-diamine · ligand · 3 copies · chains A, B, C
GOL · Glycerol · additive · 2 copies · chains A, C

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	807	0.77	0.81	78	empty
2	614	0.71	0.79	54	6FD
3	452	0.70	0.80	47	6FD
4	213	0.67	0.85	25	6FD
5	168	0.49	0.77	21	empty

Interfaces

3 interfaces between chains.

B–C · 391 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 307 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 119 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5J1V · Crystal structure of human CLK1 in complex with pyrido[3,4-g]quinazoline derivative ZW29… · the same entry in another collection · chain A against A, TM-score 1.00
P49759 · AlphaFold monomer V2.0 prediction for dual specificity protein kinase CLK1 (P49759) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P49759
Elsewhere: RCSB PDB 5J1V · PDBe 5J1V · UniProt P49759

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