MolNFT v1 · #162470 · protein

Human tnik in complex with compound 9

6RA5 · TRAF2 and nck-interacting protein kinase: “Human tnik in complex with compound 9”. X-ray diffraction, 2 ligands (JWE, MG), 5 pockets (best druggability 0.70). MolNFT v1 #162470 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6RA5
Type: protein
Length: 578 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRAF2 and nck-interacting protein kinase
EC: 2.7.11.1
UniProt: Q9UKE5
Ligands: JWE, MG
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TRAF2 and nck-interacting protein kinase (EC 2.7.11.1)	protein	295	37% helix, 18% strand	Q9UKE5
B	TRAF2 and nck-interacting protein kinase (EC 2.7.11.1)	protein	283	40% helix, 18% strand	Q9UKE5

Ligands and binding sites

JWE · 5-bromanyl-2-(2-fluoranylpyridin-4-yl)-1,7-naphthyridin-8-amine · ligand · chains A
MG · Magnesium ion · metal · chains B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	396	0.70	0.82	61	empty
2	104	0.64	0.89	26	empty
3	204	0.60	0.81	30	JWE
4	154	0.47	0.76	18	empty
5	86	0.35	0.75	21	empty

Interfaces

1 interface between chains.

A–B · 446 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (phosphorylation).

Compared structures

6RA5 · Human tnik in complex with compound 9 · the same entry in another collection · chain A against A, TM-score 1.00
Q9UKE5 · AlphaFold monomer V2.0 prediction for TRAF2 and nck-interacting protein kinase (Q9UKE5) · a predicted model of the same protein · chain B 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 Q9UKE5
Elsewhere: RCSB PDB 6RA5 · PDBe 6RA5 · UniProt Q9UKE5

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