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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:

1a8t

2.550 Å

X-ray

1998-03-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Metallo-beta-lactamase type 2
ID:BLAB_BACFG
AC:P25910
Organism:Bacteroides fragilis
Reign:Bacteria
TaxID:817
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:4.704
Number of residues:29
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: ZN ZN

Cavity properties

LigandabilityVolume (Å3)
0.724496.125

% Hydrophobic% Polar
56.4643.54
According to VolSite

Ligand :
1a8t_1 Structure
HET Code: 061
Formula: C26H23N6O2
Molecular weight: 451.500 g/mol
DrugBank ID: -
Buried Surface Area:51.48 %
Polar Surface area: 105.67 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 1
Rings: 5
Aromatic rings: 4
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
7.9497438.4839-1.14621


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
C9CG2ILE- 293.340Hydrophobic
C23CE3TRP- 323.780Hydrophobic
C24CBTRP- 324.380Hydrophobic
C13CG1VAL- 353.350Hydrophobic
C27CGPRO- 363.880Hydrophobic
O30OD1ASP- 1683.5168.5H-Bond
(Ligand Donor)
O30OD2ASP- 1682.75132.3H-Bond
(Ligand Donor)
C31CG2THR- 1714.410Hydrophobic
C6CBASN- 1763.650Hydrophobic
C17CBASN- 1763.650Hydrophobic
N1ZN ZN- 2522.360Metal Acceptor
DuArZN ZN- 2523.4893.37Pi/Cation