In Silico Investigation of Potential Pyruvate Kinase M2 Regulators from Traditional Chinese Medicine against Cancers

Table 2

H-bond occupancy for key residues of PKM2 protein with top TCM compounds overall 10,000 ps of molecular dynamics simulation.

Ligand	H-bond	Ligand atoms	Amino acid	Distance (nm)			Occupancy (%)
				Max.	Min.	Average
Saussureamine C	1	O23	A:Lys311:HZ3	0.553	0.259	0.438	15.80%
	2	O24	A:Lys311:HZ3	0.57	0.146	0.294	94.80%
	3	N27	A:Lys311:HZ3	0.593	0.234	0.408	30.00%
	4	O28	B:Lys311:HZ3	0.726	0.161	0.519	10.40%
	5	O28	B:Lys311:HZ3	0.63	0.15	0.31	73.20%
	6	H50	B:Lys311:NZ	0.76	0.24	0.43	46.20%
	7	H50	A:Asn350:OD1	0.64	0.16	0.36	44.80%
	8	H52	B:Asp354:OD1	0.54	0.27	0.31	96.20%
	9	H50	B:Asp354:OD1	0.66	0.19	0.49	20.40%
	10	H50	B:Asp354:OD2	0.79	0.15	0.51	23.20%
Precatorine	1	O18	A:Lys311:HZ3	0.39	0.14	0.29	98%
	2	O19	B:His29:HE2	0.41	0.15	0.19	97%
	3	O20	B:Tyr390:HN	0.58	0.17	0.24	91%
	4	H29	B:Leu353:O	0.52	0.16	0.37	25%
NZT*	1	O12	A:Tyr390:HN	0.32	0.16	0.19	100%
	2	O13	A:Tyr390:HN	0.46	0.17	0.37	15%
	3	O22	B:Lys311:HZ3	0.78	0.15	0.42	53%
	4	N28	B:Gln393:HE22	1.03	0.23	0.56	18%
	5	N30	B:Gln393:HE22	0.99	0.19	0.49	40%
	6	H41	A:Leu353:O	0.30	0.16	0.20	100%

H-bond occupancy cutoff: 0.35 nm.
*Control: N-(4-((4-(pyrazin-2-yl)piperazin-1-yl)carbonyl)phenyl)quinoline-8-sulfonamide.