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Crystal structure of NEK7 bound to compound 51

Analyse Crystal structure of NEK7 bound to compound 51 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6S75
Type: protein
Length: 1,051 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase NEK7
EC: 2.7.11.1
UniProt: Q8TDX7
Ligands: F9N
Pockets: 13 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase NEK7 (EC 2.7.11.1)	protein	267	43% helix, 14% strand	Q8TDX7
B	SERINE/THREONINE-protein kinase NEK7 (EC 2.7.11.1)	protein	267	38% helix, 15% strand	Q8TDX7
C	SERINE/THREONINE-protein kinase NEK7 (EC 2.7.11.1)	protein	263	37% helix, 13% strand	Q8TDX7
D	SERINE/THREONINE-protein kinase NEK7 (EC 2.7.11.1)	protein	254	39% helix, 10% strand	Q8TDX7

Ligands and binding sites

F9N · 3-[[6-(cyclohexylmethoxy)-7~{H}-purin-2-yl]amino]-~{N}-[3-(dimethylamino)propyl]benzenesulfonamide · ligand · 3 copies · chains A, B, C

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	883	0.75	0.78	84	F9N
2	693	0.73	0.79	66	F9N
3	490	0.69	0.79	54	F9N
4	500	0.67	0.78	58	empty
5	221	0.53	0.77	30	empty

Interfaces

4 interfaces between chains.

A–B · 643 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 160 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 121 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 87 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6S75 · Crystal structure of Nek7 bound to compound 51 · the same entry in another collection · chain D against D, TM-score 1.00
Q8TDX7 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase NEK7 (Q8TDX7) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q8TDX7
Elsewhere: RCSB PDB 6S75 · PDBe 6S75 · UniProt Q8TDX7

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