Skip to main content

Table 4 HMG-CoAR binding site residues involved in docking interactions with pravastatin and dipeptides, with docking scores

From: Inhibition of 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase enzyme by dipeptides identified in dry-cured ham

Pravastatin Binding energy (kcal/mol) Inhibition constant Protein residues involved in H-bond interactions (chain:residue) No. of H bonds Protein residues involved in hydrophobic interactions (chain:residue) Protein residues involved in salt bridges (chain:residue)
AA −10.13 37,85 (nM) C:Ser684 (Donor,sd)
C:Asp690 (Acceptor)
C:Asp690 (Acceptor)
C:Asp690 (Donor)
C:Lys691 (Donor,sd)
C:Lys692 (Donor,sd)
D:Glu559 (Acceptor,sd)
D:Asn755 (Donor,sd)
8 C:Asn658
C:Lys662
D:His752
D:Leu853
D:Leu862
D:Leu862
D:Val863
D:Val863
C:Arg590 (Carboxilate)
C:Lys692 (Carboxilate)
D:Lys735 (Carboxilate)
AL −6.47 18.03 (μM) C:Ser684 (Donor,sd)
C:Lys691 (Donor,sd)
D:Glu559 (Acceptor,sd)
D:Ala751 (Acceptor)
D:Asn755 (Donor,sd)
5 D:His752
D:Leu853
D:Leu862
C:Arg590 (Carboxilate)
C:Lys692 (Carboxilate)
D:Lys735 (Carboxilate)
AQ −6.41 20.08 (μM) C:Asp690 (Acceptor,sd)
D:Glu559 (Acceptor,sd)
D:Glu559 (Acceptor,sd)
D:His752 (Donor,sd)
D:Asn755 (Donor,sd)
5 C:Asp690
C:Lys691
D:His752
C:Arg590 (Carboxilate)
DA −6.58 15.08 (μM) C:Asn658 (Acceptor,sd)
C:Asn658 (Acceptor,sd)
C:Ser661 (Donor,sd)
C:Lys662 (Donor,sd)
D:Gly560 (Acceptor)
D:Leu862 (Acceptor)
6 D:Glu559
D:Val863
C:Arg590 (Carboxilate)
DD −6.92 8.51 (μM) C:Ser684 (Donor,sd)
C:Asp690 (Acceptor,sd)
D:Glu559 (Acceptor,sd)
D:Glu559 (Acceptor,sd)
D:Ala751 (Acceptor)
D:Asn755 (Donor,sd)
6 C:Lys691
D:His752
C:Arg590 (Carboxilate)
C:Lys691 (Carboxilate)
C:Lys692 (Carboxilate)
D:Lys735 (Carboxilate)
EE −7.03 7.03 (μM) C:Arg590 (Donor,sd)
C:Arg590 (Donor,sd)
C:Ser661 (Donor,sd)
C:Ser684 (Donor,sd)
C:Asp690 (Acceptor,sd)
C:Lys691 (Donor,sd)
D:Glu559 (Acceptor,sd)
D:Ala751 (Acceptor)
8 D:Leu853 C:Arg590 (Carboxilate)
C:Arg590 (Carboxilate)
C:Lys692 (Carboxilate)
C:Lys692 (Carboxilate)
D:Lys735 (Carboxilate)
ES −8.52 569.34 (nM) C:Asn658 (Donor,sd)
C:Ser661 (Donor,sd)
C:Ser684 (Donor,sd)
D:Glu559 (Acceptor,sd)
D:Glu559 (Acceptor,sd
D:Asn755 (Donor,sd)
6 D:Leu853 C:Arg590 (Carboxilate)
C:Arg590 (Carboxilate)
C:Lys691 (Carboxilate)
C:Lys692 (Carboxilate)
D:Lys735 (Carboxilate)
D:Lys752 (Carboxilate)
LL −6.83 9.85 (μM) C:Arg590 (Donor,sd)
C:Asn658 (Acceptor,sd)
C:Ser661 (Donor,sd)
C:Ser684 (Donor,sd)
C:Lys691 (Donor,sd)
C:Lys692 (Donor,sd)
D:Ala751 (Acceptor,sd)
D:Ala751 (Acceptor,sd)
D:Asn755 (Donor,sd)
9 D:Leu862 C:Arg590 (Carboxilate)
C:Arg590 (Carboxilate)
C:Lys692 (Carboxilate)
D:Lys735 (Carboxilate)
QQ −6.69 12.46 (μM) C:Asp690 (Acceptor,sd)
D:Glu559 (Acceptor,sd)
D:Glu559 (Acceptor,sd)
D:His752 (Donor,sd)
D:Asn755 (Donor,sd)
5 C:Lys691
D:His752
C:Arg590 (Carboxilate)
VH −5.91 46.66 (μM) C:Arg590 (Donor,sd)
C:Ser684 (Donor,sd)
C:Asp690 (Acceptor)
C:Asp690 (Acceptor,sd)
C:Lys692 (Donor,sd)
D:Gly560 (Acceptor)
D:Ser565 (Acceptor,sd)
D:Ser565 (Donor,sd)
D:Lys735 (Donor,sd)
D:His752 (Donor,sd)
D:Asn755 (Donor.sd)
11 D:Leu853 C:Lys691 (Carboxilate)
Ligand −6.53 16.3 (μM) C:Arg590 (Donor,sd)
C:Asn658 (Acceptor,sd)
C:Asn658 (Acceptor,sd)
C:Asn658 (Donor,sd)
C:Ser661 (Donor,sd)
C:Lys691 (Donot,sd)
D:Glu559 (Acceptor,sd)
D:Gly560 (Acceptor)
8   C:Arg590 (Carboxilate)
  1. Key residues of the binding site are highlighted in bold. Common residues whereby pravastatin and dipeptides interact with are coloured in purple