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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:

2ydx

2.800 Å

X-ray

2011-03-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Methionine adenosyltransferase 2 subunit beta
ID:MAT2B_HUMAN
AC:Q9NZL9
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
D54 %
E46 %


Ligand binding site composition:

B-Factor:78.118
Number of residues:23
Including
Standard Amino Acids: 22
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1091302.750

% Hydrophobic% Polar
47.4152.59
According to VolSite

Ligand :
2ydx_9 Structure
HET Code: STL
Formula: C14H12O3
Molecular weight: 228.243 g/mol
DrugBank ID: DB02709
Buried Surface Area:80.59 %
Polar Surface area: 60.69 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 3
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
3.86606-62.7521-35.954


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
C9CDARG- 973.70Hydrophobic
C13CGARG- 983.680Hydrophobic
O2OGSER- 1362.62143.51H-Bond
(Protein Donor)
C3CBSER- 1364.110Hydrophobic
O3OD2ASP- 1373.5150.58H-Bond
(Ligand Donor)
O3OD1ASP- 1372.7146.09H-Bond
(Ligand Donor)
O2OHTYR- 1592.53149.35H-Bond
(Ligand Donor)
C6CBILE- 1844.010Hydrophobic
C10CBALA- 1963.570Hydrophobic