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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:

3wd2

2.200 Å

X-ray

2013-06-06

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:26.595
Number of residues:32
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.161810.000

% Hydrophobic% Polar
44.1755.83
According to VolSite

Ligand :
3wd2_1 Structure
HET Code: A1L
Formula: C24H32N9O3
Molecular weight: 494.569 g/mol
DrugBank ID: -
Buried Surface Area:56.8 %
Polar Surface area: 177.9 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 5
Rings: 2
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 2
Rule of Five Violation: 1
Rotatable Bonds: 14

Mass center Coordinates

XYZ
-21.70451.70069-29.0829


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
C6CE3TRP- 974.320Hydrophobic
C5CBTRP- 974.470Hydrophobic
C4CD2TRP- 974.010Hydrophobic
N4OE2GLU- 1442.74164.84H-Bond
(Ligand Donor)
N3OE2GLU- 1443.35135.47H-Bond
(Ligand Donor)
N3OE1GLU- 1442.71159.21H-Bond
(Ligand Donor)
O3OHTYR- 2142.82164.67H-Bond
(Protein Donor)
C21CGPRO- 2193.520Hydrophobic
O2NH2ARG- 2942.7149.86H-Bond
(Protein Donor)
C18CBASP- 3164.490Hydrophobic
C21CDARG- 3383.790Hydrophobic
C22CBARG- 3383.940Hydrophobic
C23CG1ILE- 3394.210Hydrophobic
N9NE1TRP- 4033.01130.25H-Bond
(Protein Donor)