Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking

BMC Structural Biology

Table 3 Docking of methyldecanoic acid butyl esters

	Experimental data	Docking into X-ray structures							No. of false predictions
Substrate		1CLE^a	1CRL	1LPM^a	1LPN^{a, b}	1LPO^a	1LPP^{a, b}	1LPS^a
(R)-2-MDB	+	+	-	-	-	+	-	-	5
(S)-2-MDB	+	+	-	-	-	-	-	-	6
(R)-3-MDB	+	+	+	-	-	+	-	-	4
(S)-3-MDB	+	+	+	-	-	+	-	-	4
(R)-4-MDB	+	+	+	-	-	+	-	-	4
(S)-4-MDB	+	+	+	-	-	+	-	-	4
(R)-5-MDB	+	+	+	-	-	+	-	-	4
(S)-5-MDB	+	+	+	-	-	+	-	-	4
(R)-6-MDB	+	+	+	+	-	+	-	-	3
(S)-6-MDB	+	+	+	+	-	+	-	-	3
(R)-7-MDB	+	+	+	-	-	+	-	-	4
(S)-7-MDB	+	+	+	-	-	+	-	-	4
(R)-8-MDB	+	+	+	-	-	+	-	-	4
(S)-8-MDB	+	+	+	-	-	+	-	-	4
Docking into substrate-imprinted structures
(R)-2-MDB	+	+	+	+	-	+	-	-	3
(S)-2-MDB	+	-	+	+	-	+	-	-	4
(R)-3-MDB	+	+	+	+	-	+	-	-	3
(S)-3-MDB	+	-	+	+	-	+	-	-	4
(R)-4-MDB	+	+	+	+	-	+	-	-	3
(S)-4-MDB	+	+	+	+	-	+	-	+	2
(R)-5-MDB	+	+	+	+	-	+	-	+	2
(S)-5-MDB	+	+	+	+	-	+	-	+	2
(R)-6-MDB	+	+	+	+	-	+	-	+	2
(S)-6-MDB	+	+	+	+	-	+	-	-	3
(R)-7-MDB	+	+	+	+	-	+	-	-	3
(S)-7-MDB	+	+	+	+	-	+	-	-	3
(R)-8-MDB	+	+	+	+	-	+	-	-	3
(S)-8-MDB	+	+	+	+	-	+	-	-	3

Docking of 2- to 8-MDB into seven CRL structures using FlexX. The substrates were docked into the not optimised X-ray structures and the substrate-imprinted structures. "+" and "-" indicate that the docking results predict 2- to 8-MDB to be a substrate or a non-substrate. Correct predictions are indicated by bold and large font type. Experimental data [41] is included for comparison. ^aStructure was resolved with an inhibitor bound. ^bDisplaced histidine.

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