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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:

1xgj

1.970 Å

X-ray

2004-09-17

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:6.0006.0006.0000.0006.0001

List of CHEMBLId :

CHEMBL1222313


Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Beta-lactamase
ID:AMPC_ECOLI
AC:P00811
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:3.5.2.6


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:15.019
Number of residues:26
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.360489.375

% Hydrophobic% Polar
29.6670.34
According to VolSite

Ligand :
1xgj_2 Structure
HET Code: HTC
Formula: C12H6NO7S2
Molecular weight: 340.309 g/mol
DrugBank ID: DB07927
Buried Surface Area:51.76 %
Polar Surface area: 185.35 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-1.022915.171574.2711


Binding mode :
What is Poseview ?
  • 2D View
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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
O23OGSER- 642.68140.76H-Bond
(Protein Donor)
O23NSER- 642.97145.56H-Bond
(Protein Donor)
O17NE2GLN- 1203.46162.97H-Bond
(Protein Donor)
O17ND2ASN- 1522.65170.29H-Bond
(Protein Donor)
S20CD2LEU- 2934.230Hydrophobic
N1OALA- 3182.67120.55H-Bond
(Ligand Donor)
O23NALA- 3182.87160.2H-Bond
(Protein Donor)
C4CG2THR- 3194.360Hydrophobic
C6CBTHR- 3194.480Hydrophobic