Effect of the explicit flexibility of the InhA enzyme from Mycobacterium tuberculosis in molecular docking simulations

Cohen, Elisangela ML; Machado, Karina S; Cohen, Marcelo; Norberto de Souza, Osmar

doi:10.1186/1471-2164-12-S4-S7

Table 4 Top 19 and 18 amino acid residues that interacted with the ligands in at least one snapshot for each of the three FFR models during the docking simulations

From: Effect of the explicit flexibility of the InhA enzyme from Mycobacterium tuberculosis in molecular docking simulations

(a)	InhA_WT - ETH				InhA_I16T - ETH				InhA_I21V - ETH
Residue	Best FEB		Best Pose		Best FEB		Best Pose		Best FEB		Best Pose
	HHB	NNB	HHB	NNB	HHB	NNB	HHB	NNB	HHB	NNB	HHB	NNB
GLY14	681	363	64	47	89	80	2	2	1,652	311	264	18
ILE15	12	164	0	0	81	41	0	0	487	39	0	0
SER20	0	856	0	100	3	0	0	6	2	99	0	0
ILE21	0	1,015	0	1,974	0	971	0	1,528	0	0	0	0
VAL21	0	0	0	0	0	0	0	0	0	714	0	1,022
PHE41	0	4	0	0	0	65	0	0	0	426	0	0
SER94	1,115	955	387	740	1,311	516	156	762	1,712	1,683	447	1,060
ILE95	323	389	392	229	713	479	74	424	110	1,566	230	617
GLY96	178	169	2	213	8	781	0	124	2	270	0	170
MET147	10	1,127	49	1,805	3	755	9	943	2	849	3	1,096
ASP148	78	394	556	587	328	512	842	348	90	104	444	537
PHE149	5	1,028	0	1,235	0	1,529	0	1,531	0	564	0	1,453
MET161	0	1,064	0	1,664	1	1,204	0	1,838	2	712	0	1,675
LYS165	0	405	0	719	0	531	0	618	0	32	0	161
ALA191	4	184	16	666	0	177	12	707	42	90	55	483
GLY192	779	68	903	155	959	140	1,586	136	564	210	1,716	384
PRO193	0	333	0	305	0	398	0	256	0	408	0	720
ILE194	275	71	0	221	27	366	10	999	5	12	73	185
THR196	71	216	4	322	0	644	0	889	2	363	0	693
(b)	InhA_WT - TCL				InhA_I16T - TCL				InhA_I21V - TCL
Residue	Best FEB		Best Pose		Best FEB		Best Pose		Best FEB		Best Pose
	HHB	NNB	HHB	NNB	HHB	NNB	HHB	NNB	HHB	NNB	HHB	NNB
GLY14	861	934	523	59	101	533	18	5	1,157	1,131	582	114
ILE16	0	494	0	85	0	0	0	0	0	571	0	191
THR16	0	0	0	0	0	433	0	38	0	0	0	0
ILE21	0	998	0	2,067	0	944	0	1,060	0	0	0	0
VAL21	0	0	0	0	0	0	0	0	0	638	0	1,200
PHE41	0	47	0	0	0	519	0	0	0	1,383	0	5
SER94	1,746	1,676	1,780	1,340	1,450	605	1,213	67	638	458	777	297
ILE95	241	562	342	450	645	1,134	259	108	438	1,022	249	242
GLY96	370	897	49	745	517	1,148	64	831	197	970	19	665
PHE97	26	71	13	103	17	31	26	1,430	2	70	7	125
MET103	2	9	0	0	0	0	0	0	13	33	105	1,370
MET147	121	541	137	910	13	507	8	268	13	257	8	341
PHE149	10	97	1	287	0	3	0	0	0	2	0	0
MET161	30	1,262	13	2,310	9	1,234	13	1,872	3	322	13	1,402
LYS165	0	176	0	570	0	111	0	203	0	0	0	2
GLY192	1,418	0	1,959	2	860	0	1,308	0	297	0	1,302	1
ILE194	1	0	8	3	2	152	6	1,830	13	0	21	17
THR196	16	55	40	269	0	276	6	438	2	86	1	499
(c)	InhA_WT - PIF				InhA_I16T - PIF				InhA_I21V - PIF
Residue	Best FEB		Best Pose		Best FEB		Best Pose		Best FEB		Best Pose
	HHB	NNB	HHB	NNB	HHB	NNB	HHB	NNB	HHB	NNB	HHB	NNB
GLY14	83	202	57	103	1	125	2	0	65	818	15	379
ILE16	0	765	0	595	0	0	0	0	0	228	0	147
THR16	0	0	0	0	0	701	0	846	0	0	0	0
ILE21	0	456	0	1,370	0	333	0	865	0	0	0	0
VAL21	0	0	0	0	0	0	0	0	0	669	0	1,547
ASP42	14	10	1	10	671	553	53	0	17	13	2	7
PHE93	1	1,050	0	0	0	0	3	7	0	0	0	0
SER94	238	386	174	1,047	170	297	71	1,043	47	1,223	79	1,952
ILE95	2	773	9	1,779	191	565	65	1,275	0	1,942	1	2,202
GLY96	316	1,252	130	2,389	911	1,110	270	1,894	1,532	1,325	333	2,291
PHE97	1	1,050	7	1,146	3	757	0	531	1	186	0	166
PHE149	0	246	0	640	0	121	0	0	0	58	0	78
MET161	0	494	1	1,491	3	854	1	1,021	0	1,436	5	1,739
LYS165	0	160	0	303	0	347	0	0	0	12	0	20
GLY192	279	1	759	3	189	9	661	14	468	21	886	31
ILE194	11	5	55	7	4	67	9	335	17	78	25	355
THR196	4	472	14	1,295	6	905	10	1,491	38	2,168	16	2,572
LEU197	3	430	0	167	4	285	0	0	5	14	0	7
ALA198	0	382	0	735	0	105	0	0	1	11	0	21

The first columns show, from the total of amino acid residues found in Table 3, the top 19 (18 for TCL) residues that were able to make contacts, HHB and/or NNB, with the ligands (a) ETH, (b) TCL, and (c) PIF, respectively, in at least 10% of the trajectories. Note that each FFR model is a MD simulation trajectory. Columns 2 to 13 show the number of snapshots for each FFR model involved in such contacts (marked in bold).

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ISSN: 1471-2164

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