MolNFT v1 · #173717 · protein

Structure of LIMK1 kinase domain with allosteric inhibitor th-470

7B8W · Lim domain kinase 1: “Structure of LIMK1 kinase domain with allosteric inhibitor th-470”. X-ray diffraction, 1 ligand (T3B), 12 pockets (best druggability 0.78). MolNFT v1 #173717 on GenesisL1: 3D structure, binding sites and…

PDB: 7B8W
Type: protein
Length: 1,103 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: T3B
Pockets: 12 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lim domain kinase 1 (EC 2.7.11.1)	protein	279	40% helix, 18% strand	P53667
B	Lim domain kinase 1 (EC 2.7.11.1)	protein	275	40% helix, 17% strand	P53667
C	Lim domain kinase 1 (EC 2.7.11.1)	protein	276	39% helix, 18% strand	P53667
D	Lim domain kinase 1 (EC 2.7.11.1)	protein	273	41% helix, 18% strand	P53667

Ligands and binding sites

T3B · 2-(2-methylpropanoylamino)-~{N}-[2-[(phenylmethyl)-[4-(phenylsulfamoyl)phenyl]carbonyl-amino]ethyl]-1,3-thiazole-5-carboxamide · ligand · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 3 copies · chains A

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

Pockets

12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	356	0.78	0.88	41	T3B
2	349	0.78	0.88	40	T3B
3	403	0.77	0.86	47	T3B
4	346	0.76	0.87	40	T3B
5	934	0.73	0.77	107	EDO

Interfaces

4 interfaces between chains.

A–B · 751 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 399 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 120 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 22 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7B8W · Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470 · 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 C 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 7B8W · PDBe 7B8W · UniProt P53667

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.