Investigating the binding affinity, molecular dynamics, and ADMET properties of 2,3-dihydrobenzofuran derivatives as an inhibitor of fungi, bacteria, and virus protein

Nath, Ashutosh; Kumer, Ajoy; Zaben, Fahmida; Khan, Md. Wahab

doi:10.1186/s43088-021-00117-8

Beni-Suef University Journal of Basic and Applied Sciences

Table 4 Nonbonding interactions of selected two DHB with six proteins (pose predicted by FireDock). CH conventional hydrogen bond, H hydrogen bond, C carbon hydrogen bond

From: Investigating the binding affinity, molecular dynamics, and ADMET properties of 2,3-dihydrobenzofuran derivatives as an inhibitor of fungi, bacteria, and virus protein

Interaction residue	Distance	Bond category	Bond type	Interaction residue	Distance	Bond category	Bond type
DHB 2 + 1kum				DHB 3 + 4k6l
TRP563	2.215	H	CH	GLY135	2.522	H	C
THR525	2.407	H	C	PRO136	1.963	H	C
SER558	2.288	H	C	LEU125	2.407	H	Pi-D H
THR525	2.607	Other	Pi-Lone Pair	PRO136	4.231	Hydrophobic	Alkyl
THR524 THR525	4.930	Hydrophobic	Amide-Pi Stacked	LEU85	4.128	Hydrophobic	Alkyl
ALA553	5.087	Hydrophobic	Alkyl	LEU125	3.829	Hydrophobic	Alkyl
ALA553	4.238	Hydrophobic	Alkyl	TRP25	5.244	Hydrophobic	Pi-Alkyl
ILE531	4.933	Hydrophobic	Alkyl
TYR556	4.083	Hydrophobic	Pi-Alkyl
TRP563	5.086	Hydrophobic	Pi-Alkyl
TRP563	4.961	Hydrophobic	Pi-Alkyl
TRP563	4.139	Hydrophobic	Pi-Alkyl
DHB 2 + 1ru7				DHB 3 +3rda
SER291	2.564	H	C	LEU63	2.524	H	CH
PRO307	2.034	H	C	ASN143	2.333	H	CH
LEU293	1.966	H	C	LEU58	2.020	G	C
CYS278	2.522	Other	Sulfur-X	ASP98	3.335	Electrostatic	Pi-Anion
LYS281	3.333	Electrostatic	Pi-Cation	ALA96	4.587	Hydrophobic	Alkyl
SER291	3.091	H	Pi-Donor H	ALA96	3.843	Hydrophobic	Alkyl
LYS281	2.484	Hydrophobic	Pi-Sigma	TRP106	4.791	Hydrophobic	Pi-Alkyl
LYS281	5.284	Hydrophobic	Alkyl	ILE95	5.495	Hydrophobic	Pi-Alkyl
PRO307	3.699	Hydrophobic	Alkyl
DHB 3 +6og7				DHB 2 + 4tyd
ASP83	1.843	H	CH	GLY137	1.318	H	CH
ARG86	2.920	H	CH	SER139	2.840	H	CH
PRO21	2.956	H	C	VAL163	3.035	H	CH
PRO21	2.124	H	C	LYS136	2.351	H	C
ASN20	2.545	H	Pi-D H	LYS136	2.994	H	C
VAL18	4.884	Hydrophobic	Alkyl	SER139	2.135	H	C
VAL18	5.293	Hydrophobic	Alkyl	GLY162	1.365	H	C
VAL19	3.656	Hydrophobic	Alkyl	HIS57	2.729	H	C
LEU23	5.444	Hydrophobic	Alkyl	LYS136	4.992	Electrostatic	Pi-Cati
TYR82	4.897	Hydrophobic	Pi-Alkyl	CYS159	5.342	Other	Pi-Sulfur
TYR82	5.358	Hydrophobic	Pi-Alkyl	VAL132	4.192	Hydrophobic	Alkyl
HIS199	5.393	Hydrophobic	Pi-Alkyl	ALA157	4.471	Hydrophobic	Alkyl
VAL19	4.222	Hydrophobic	Pi-Alkyl	CYS159	3.009	Hydrophobic	Alkyl
				HIS57	4.399	Hydrophobic	Pi-Alkyl
				PHE154	3.796	Hydrophobic	Pi-Alkyl
				LYS136	5.418	Hydrophobic	Pi-Alkyl
				ALA156	5.132	Hydrophobic	Pi-Alkyl
				ALA157	3.578	Hydrophobic	Pi-Alkyl
DHB 2 + 3rda				DHB 8 + 3rda
ASN180	2.082	H	CH	ASN180	2.497	H	CH
ASN224	1.866	H	CH	PHE187	3.781	Hydrophobic	Pi-Pi Stacked
PHE187	3.674	Hydrophobic	Pi-Pi Stacked	PHE187	4.996	Hydrophobic	Pi-Alkyl
ARG232	4.106	Hydrophobic	Alkyl	TYR225	4.896	Hydrophobic	Pi-Alkyl
PHE187	5.312	Hydrophobic	Pi-Alkyl
TYR225	5.360	Hydrophobic	Pi-Alkyl

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