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The LIMK1 kinase domain bound to LIJTF500025

Analyse The LIMK1 kinase domain bound to LIJTF500025 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ATU
Type: protein
Length: 1,050 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lim domain kinase 1
EC: 2.7.11.1
UniProt: P53667
Ligands: RXN
Pockets: 12 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lim domain kinase 1 (EC 2.7.11.1)	protein	276	38% helix, 12% strand	P53667
B	Lim domain kinase 1 (EC 2.7.11.1)	protein	287	39% helix, 15% strand	P53667
C	Lim domain kinase 1 (EC 2.7.11.1)	protein	244	43% helix, 12% strand	P53667
D	Lim domain kinase 1 (EC 2.7.11.1)	protein	243	41% helix, 14% strand	P53667

Ligands and binding sites

RXN · (S)-2-benzyl-6-(8-chloro-5-methyl-4-oxo-2,3,4,5-tetrahydrobenzo[b][1,4]oxazepin-3-yl)-7-oxo-4,5,6,7-tetrahydro-2H-pyrazolo[3,4-c]pyridine-3-carboxamide · ligand · 4 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	478	0.79	0.86	59	RXN
2	454	0.78	0.86	54	RXN
3	432	0.75	0.84	51	RXN
4	338	0.71	0.83	41	RXN
5	687	0.70	0.77	73	empty

Interfaces

3 interfaces between chains.

A–B · 802 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 596 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 188 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

7ATU · The LIMK1 Kinase Domain Bound To LIJTF500025 · the same entry in another collection · chain D against D, TM-score 1.00
P53667 · AlphaFold monomer V2.0 prediction for lim domain kinase 1 (P53667) · a predicted model of the same protein · chain D against A, TM-score 0.94

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 P53667
Elsewhere: RCSB PDB 7ATU · PDBe 7ATU · UniProt P53667

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