Treatment of Cardiovascular Disease by Traditional Chinese Medicine against Pregnane X Receptor

Table 2

H-bond occupancy for key residues of PXR protein complex with the top three candidates and PNU-142721 over 40 ns molecular dynamics simulation.

Ligand	H-bond	Ligand atom	Amino acid	Distance (nm)			Occupancy (%)
				Max.	Min.	Average
BEMG	1	O25	Ser247:HG1	0.62	0.18	0.36	12.85%
	2	O26	Ser247:HG1	0.90	0.19	0.49	7.60%
	3	O17	Ser247:HG1	0.91	0.18	0.48	4.40%
	4	O27	Ser247:HG1	0.86	0.19	0.47	4.00%
	5	O17	Gln285:HE22	1.08	0.17	0.32	59.90%
	6	O27	Gln285:HE22	0.89	0.18	0.36	31.45%
	7	H41	Gln285:OE1	1.00	0.16	0.54	9.75%
	8	H49	Gln285:NE2	1.07	0.24	0.55	1.95%
	9	O28	His407:HE2	0.89	0.18	0.42	18.95%
	10	O19	His407:HE2	0.88	0.20	0.56	4.20%
	11	O25	His407:HE2	0.61	0.21	0.40	5.75%
	12	H52	His407:ND1	0.78	0.20	0.47	1.80%
Ixerisoside	1	H57	Ser208:O	0.57	0.15	0.21	95.70%
	2	O19	Arg203:HH22	1.55	0.16	0.58	7.15%
	3	H57	Ser208:OG	0.90	0.17	0.50	6.85%
	4	O19	Arg203:HH12	1.66	0.16	0.77	2.45%
	5	O29	Gln285:HE22	0.99	0.18	0.52	6.45%
	6	H55	Gln285:OE1	0.99	0.18	0.60	3.45%
	7	O22	Gln285:HE22	0.91	0.21	0.65	0.50%
	8	H55	Trp299:NE1	0.98	0.21	0.55	5.50%
	9	H56	Trp299:NE1	0.69	0.23	0.45	1.55%
Tangshenoside II	1	H46	Gln285:OE1	0.61	0.15	0.25	84.20%
	2	O8	Gln285:HE22	0.50	0.17	0.26	78.75%
	3	O23	Gln285:HE22	0.51	0.17	0.26	76.70%
	4	O9	Gln285:HE22	0.57	0.20	0.38	13.40%
	5	O7	Gln285:HE22	0.75	0.23	0.47	1.00%
	6	O7	Ser247:HG1	0.67	0.19	0.46	1.10%
	7	O26	Ser247:HG1	0.85	0.19	0.59	0.30%
	8	H43	Trp299:NE1	0.71	0.19	0.28	71.05%
	9	H45	Trp299:NE1	0.69	0.22	0.44	6.50%
	10	O26	His407:HE2	0.70	0.17	0.42	38.05%
PNU-142721	1	N9	Gln285:HE22	1.03	0.17	0.50	2.40%
	2	H28	His407:ND1	0.82	0.19	0.30	54.55%
	3	H28	His407:O	1.05	0.20	0.31	44.55%
	4	H28	His407:NE2	0.65	0.24	0.37	5.60%

H-bond occupancy cutoff: 0.3 nm.