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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

1qay

2.800 Å

X-ray

1999-04-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:3-hydroxy-3-methylglutaryl-coenzyme A reductase
ID:MVAA_PSEMV
AC:P13702
Organism:Pseudomonas mevalonii
Reign:Bacteria
TaxID:32044
EC Number:1.1.1.88


Chains:

Chain Name:Percentage of Residues
within binding site
A71 %
B29 %


Ligand binding site composition:

B-Factor:27.291
Number of residues:24
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors: NAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.733445.500

% Hydrophobic% Polar
56.0643.94
According to VolSite

Ligand :
1qay_1 Structure
HET Code: MEV
Formula: C6H11O4
Molecular weight: 147.149 g/mol
DrugBank ID: DB03518
Buried Surface Area:74.52 %
Polar Surface area: 80.59 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 0
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
85.8527125.476108.867


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
O8OE2GLU- 833.15136.9H-Bond
(Ligand Donor)
O3NH1ARG- 2613.45131.8H-Bond
(Protein Donor)
O3NH2ARG- 2612.81170.79H-Bond
(Protein Donor)
O3CZARG- 2613.570Ionic
(Protein Cationic)
C4CG2THR- 2643.570Hydrophobic
C8CDLYS- 2674.010Hydrophobic
O8NZLYS- 2673.2125.96H-Bond
(Protein Donor)
C6CBALA- 3683.380Hydrophobic
C6CD1LEU- 3724.160Hydrophobic
C6CD1ILE- 3773.920Hydrophobic
C2CD1ILE- 7134.360Hydrophobic
C3CG1ILE- 7134.40Hydrophobic
C2C4NNAD- 10013.770Hydrophobic