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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:

1o6i

1.700 Å

X-ray

2002-10-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Chitinase B
ID:CHIB_SERMA
AC:P11797
Organism:Serratia marcescens
Reign:Bacteria
TaxID:615
EC Number:3.2.1.14


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:18.633
Number of residues:22
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.8551559.250

% Hydrophobic% Polar
45.6754.33
According to VolSite

Ligand :
1o6i_1 Structure
HET Code: 0HZ
Formula: C11H20N5O2
Molecular weight: 254.309 g/mol
DrugBank ID: -
Buried Surface Area:52.42 %
Polar Surface area: 113.04 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 4
Rings: 2
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
17.076242.2609102.882


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
CBCE1TYR- 103.880Hydrophobic
CGCZTYR- 103.550Hydrophobic
CB1CE2PHE- 514.280Hydrophobic
O1NTRP- 972.72163.8H-Bond
(Protein Donor)
CGCBALA- 1843.870Hydrophobic
CGSDMET- 2123.50Hydrophobic
OOHTYR- 2142.7152.63H-Bond
(Protein Donor)
CBCE3TRP- 4034.060Hydrophobic
CB1CZ2TRP- 4033.490Hydrophobic