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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:

2wya

1.700 Å

X-ray

2009-11-13

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Hydroxymethylglutaryl-CoA synthase, mitochondrial
ID:HMCS2_HUMAN
AC:P54868
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.3.3.10


Chains:

Chain Name:Percentage of Residues
within binding site
B2 %
C98 %


Ligand binding site composition:

B-Factor:16.413
Number of residues:49
Including
Standard Amino Acids: 47
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.305405.000

% Hydrophobic% Polar
56.6743.33
According to VolSite

Ligand :
2wya_3 Structure
HET Code: HMG
Formula: C27H39N7O20P3S
Molecular weight: 906.620 g/mol
DrugBank ID: DB03169
Buried Surface Area:57.28 %
Polar Surface area: 490.04 Å2
Number of
H-Bond Acceptors: 25
H-Bond Donors: 6
Rings: 3
Aromatic rings: 2
Anionic atoms: 5
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 24

Mass center Coordinates

XYZ
21.3703100.72-29.6403


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
N6AOALA- 813.25130.33H-Bond
(Ligand Donor)
O4ANZLYS- 833.710Ionic
(Protein Cationic)
C5BCD2LEU- 884.320Hydrophobic
CCPCD2LEU- 884.470Hydrophobic
CDPCD2LEU- 884.450Hydrophobic
O4NCYS- 1663.16145.22H-Bond
(Protein Donor)
C4SGCYS- 1663.710Hydrophobic
O5AND2ASN- 2042.83164.74H-Bond
(Protein Donor)
OAPOASN- 2042.71169.55H-Bond
(Ligand Donor)
CAPCBALA- 2054.450Hydrophobic
N8POG1THR- 2083.25125.72H-Bond
(Ligand Donor)
C4CE1PHE- 2413.570Hydrophobic
C6CD1PHE- 2414.120Hydrophobic
C6PCG2VAL- 2533.820Hydrophobic
N4POGSER- 2582.86166.9H-Bond
(Ligand Donor)
S1PCBSER- 2583.560Hydrophobic
CDPCD1ILE- 2594.260Hydrophobic
CEPCD1ILE- 2594.20Hydrophobic
C2PCG1ILE- 2594.220Hydrophobic
C2PCBTYR- 2624.110Hydrophobic
O7NE2HIS- 3012.93148.15H-Bond
(Protein Donor)
C2PCGPRO- 3034.060Hydrophobic
CDPCE2PHE- 3043.40Hydrophobic
O9ANZLYS- 3063.910Ionic
(Protein Cationic)
C2PSDMET- 3074.460Hydrophobic
O7ANZLYS- 3102.92123.56H-Bond
(Protein Donor)
O9ANZLYS- 3102.59155.79H-Bond
(Protein Donor)
O7ANZLYS- 3102.920Ionic
(Protein Cationic)
O9ANZLYS- 3102.590Ionic
(Protein Cationic)
O7ND2ASN- 3803.11168.54H-Bond
(Protein Donor)
C4CE1TYR- 3824.10Hydrophobic
S1PCE2TYR- 4124.030Hydrophobic
C2CD2TYR- 4123.860Hydrophobic
C4CBSER- 4144.440Hydrophobic
O4NSER- 4142.84174.14H-Bond
(Protein Donor)