Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3for

1.930 Å

X-ray

2008-12-31

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:5.1205.1205.1200.0005.1201

List of CHEMBLId :

CHEMBL1236974


Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Thermolysin
ID:THER_BACTH
AC:P00800
Organism:Bacillus thermoproteolyticus
Reign:Bacteria
TaxID:1427
EC Number:3.4.24.27


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:17.527
Number of residues:26
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.287408.375

% Hydrophobic% Polar
45.4554.55
According to VolSite

Ligand :
3for_1 Structure
HET Code: ZNP
Formula: C10H12N2O3
Molecular weight: 208.214 g/mol
DrugBank ID: -
Buried Surface Area:56.87 %
Polar Surface area: 88.91 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 1
Rings: 1
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-9.6564-39.3821-3.43307


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
OAOND2ASN- 1123.01162.27H-Bond
(Protein Donor)
CAJCD2LEU- 1334.230Hydrophobic
CAHCG2VAL- 1393.380Hydrophobic
CAGCBHIS- 1424.170Hydrophobic
CAHCG2ILE- 1883.890Hydrophobic
CAJCD2LEU- 2023.440Hydrophobic
NAKZN ZN- 8052.770Metal Acceptor
OANZN ZN- 8052.250Metal Acceptor
OAMZN ZN- 8052.630Metal Acceptor