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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:

5c8y

2.590 Å

X-ray

2015-06-26

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Tubulin tyrosine ligase
ID:E1BQ43_CHICK
AC:E1BQ43
Organism:Gallus gallus
Reign:Eukaryota
TaxID:9031
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
F100 %


Ligand binding site composition:

B-Factor:87.760
Number of residues:26
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.882651.375

% Hydrophobic% Polar
50.2649.74
According to VolSite

Ligand :
5c8y_1 Structure
HET Code: ACP
Formula: C11H14N5O12P3
Molecular weight: 501.176 g/mol
DrugBank ID: DB03909
Buried Surface Area:59.99 %
Polar Surface area: 310.64 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-8.65865-50.7017100.077


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
O1BNZLYS- 743.90Ionic
(Protein Cationic)
O2BNZLYS- 743.090Ionic
(Protein Cationic)
O2ANZLYS- 743.50Ionic
(Protein Cationic)
O2BNZLYS- 743.09163.63H-Bond
(Protein Donor)
N6OE1GLN- 1832.9169.49H-Bond
(Ligand Donor)
N6OLYS- 1843.15147.52H-Bond
(Ligand Donor)
N1NLEU- 1863.34159.88H-Bond
(Protein Donor)
C4'CD2LEU- 2404.330Hydrophobic
C1'CD2LEU- 2404.390Hydrophobic
O3'NTHR- 2413.14152.42H-Bond
(Protein Donor)
O1GND2ASN- 3332.59155.62H-Bond
(Protein Donor)