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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:

5ca1

2.400 Å

X-ray

2015-06-29

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Tubulin beta-2 chain
ID:TBB2_CHICK
AC:P32882
Organism:Gallus gallus
Reign:Eukaryota
TaxID:9031
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:31.719
Number of residues:33
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.641533.250

% Hydrophobic% Polar
66.4633.54
According to VolSite

Ligand :
5ca1_1 Structure
HET Code: NZO
Formula: C14H11N3O3S
Molecular weight: 301.320 g/mol
DrugBank ID: DB08313
Buried Surface Area:71.91 %
Polar Surface area: 112.32 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-16.196565.3474-37.68


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
C14CBGLN- 1344.190Hydrophobic
O3ND2ASN- 1653.19157.37H-Bond
(Protein Donor)
C14CZPHE- 1673.980Hydrophobic
N3OE1GLU- 1982.7136.25H-Bond
(Ligand Donor)
N2OE2GLU- 1982.84172.3H-Bond
(Ligand Donor)
N2OE1GLU- 1982.97120.51H-Bond
(Ligand Donor)
C14CG2THR- 2373.810Hydrophobic
C7CBCYS- 2394.050Hydrophobic
C14CD1LEU- 2404.440Hydrophobic
SCD2LEU- 2463.470Hydrophobic
C14CD2LEU- 2504.210Hydrophobic
C7CD1LEU- 2534.140Hydrophobic
C9CD1LEU- 2533.880Hydrophobic
SCD2LEU- 2534.490Hydrophobic
C11CD2LEU- 2533.830Hydrophobic
C10CGMET- 2574.140Hydrophobic
C11CBALA- 3143.850Hydrophobic
SCBALA- 3143.790Hydrophobic
C11CD1ILE- 3683.990Hydrophobic