In Silico Investigation of Potential TRAF6 Inhibitor from Traditional Chinese Medicine against Cancers

Table 2

H-bond occupancy for key residues of TRAF6 protein with top three TCM candidates over 10 ns of MD simulation.

Ligand	H-bond	Ligand atom	Amino acid	Distance (nm)			Occupancy (%)
				Max.	Min.	Average
Tryptophan	1	H27	Glu59:OE1	2.93	0.15	0.95	13.0%
	2	H27	Glu59:OE2	2.729	0.152	0.901	32.6%
	3	H20	Glu69:OE1	2.68	0.163	1.229	0.8%
	4	H20	Glu69:OE2	2.671	0.17	1.214	1.0%
	5	H27	Glu69:OE1	2.427	0.146	0.933	29.6%
	6	H27	Glu69:OE2	2.318	0.148	0.926	25.4%
Diiodotyrosine	1	H24	Glu69:OE1	0.55	0.15	0.30	77%
	2	H24	Glu69:OE2	0.56	0.15	0.30	82%
	3	H24	Leu74:O	0.92	0.27	0.59	14.2%
Saussureamine C	1	H50	Leu64:O	1.13	0.16	0.44	45.0%
	2	H50	Glu69:OE1	0.69	0.16	0.44	19.6%
	3	H50	Glu69:OE2	0.72	0.15	0.46	17.8%
	4	H52	Glu69:OE1	0.44	0.15	0.23	95.6%
	5	H52	Glu69:OE2	0.38	0.15	0.24	85.8%

H-bond occupancy cut-off is 0.35 nm.