MolNFT v1 · #111062 · protein

TNNI3K complexed with inhibitor 1

4YFI · SERINE/THREONINE-protein kinase TNNI3K: “TNNI3K complexed with inhibitor 1”. X-ray diffraction, 1 ligand (4CW), 11 pockets (best druggability 0.84). MolNFT v1 #111062 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4YFI
Type: protein
Length: 1,060 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase TNNI3K
EC: 2.7.11.1
UniProt: Q59H18
Ligands: 4CW
Pockets: 11 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase TNNI3K (EC 2.7.11.1)	protein	268	46% helix, 18% strand	Q59H18
B	SERINE/THREONINE-protein kinase TNNI3K (EC 2.7.11.1)	protein	262	45% helix, 18% strand	Q59H18
C	SERINE/THREONINE-protein kinase TNNI3K (EC 2.7.11.1)	protein	269	45% helix, 17% strand	Q59H18
D	SERINE/THREONINE-protein kinase TNNI3K (EC 2.7.11.1)	protein	261	44% helix, 18% strand	Q59H18

Ligands and binding sites

4CW · N-methyl-3-(9H-purin-6-ylamino)benzenesulfonamide · ligand · 4 copies · chains A, B, C, D

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

Pockets

11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	608	0.84	0.89	69	empty
2	62	0.70	0.96	19	empty
3	253	0.69	0.85	33	4CW
4	532	0.69	0.78	83	empty
5	264	0.68	0.84	33	4CW

Interfaces

6 interfaces between chains.

C–D · 2128 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2117 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 706 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 406 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 393 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4YFI · TNNI3K complexed with inhibitor 1 · the same entry in another collection · chain D against D, TM-score 1.00
Q59H18 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase TNNI3K (Q59H18) · a predicted model of the same protein · chain A 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 Q59H18
Elsewhere: RCSB PDB 4YFI · PDBe 4YFI · UniProt Q59H18

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