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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:

1hlk

2.500 Å

X-ray

2000-12-01

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:39.886
Number of residues:24
Including
Standard Amino Acids: 22
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: ZN ZN

Cavity properties

LigandabilityVolume (Å3)
0.342492.750

% Hydrophobic% Polar
51.3748.63
According to VolSite

Ligand :
1hlk_1 Structure
HET Code: 113
Formula: C15H13O8
Molecular weight: 321.259 g/mol
DrugBank ID: DB02593
Buried Surface Area:47.11 %
Polar Surface area: 125.35 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 2
Rings: 3
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-8.72852-28.711317.5705


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
C1CD1ILE- 464.210Hydrophobic
C2CBTRP- 494.030Hydrophobic
C12CE3TRP- 494.170Hydrophobic
C12CG1VAL- 524.320Hydrophobic
O30NZLYS- 1843.770Ionic
(Protein Cationic)
C22CBSER- 1904.210Hydrophobic
O16ND2ASN- 1933.43131.05H-Bond
(Protein Donor)
O30NASN- 1933.05140.64H-Bond
(Protein Donor)
C6CBASN- 1933.610Hydrophobic
O19ZN ZN- 10022.560Metal Acceptor