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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:

4b8l

3.000 Å

X-ray

2012-08-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Aurora kinase B-A
ID:AUKBA_XENLA
AC:Q6DE08
Organism:Xenopus laevis
Reign:Eukaryota
TaxID:8355
EC Number:2.7.11.1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:58.881
Number of residues:27
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.948462.375

% Hydrophobic% Polar
56.2043.80
According to VolSite

Ligand :
4b8l_1 Structure
HET Code: A0P
Formula: C10H13N6O12P3
Molecular weight: 502.164 g/mol
DrugBank ID: DB04395
Buried Surface Area:50.19 %
Polar Surface area: 322.68 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
22.654913.99922.0862


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
O2'OLEU- 993.14159.89H-Bond
(Ligand Donor)
C1'CBLEU- 994.160Hydrophobic
O1BNZLYS- 1223.30Ionic
(Protein Cationic)
O2BNZLYS- 1223.120Ionic
(Protein Cationic)
O2ANZLYS- 1223.480Ionic
(Protein Cationic)
O2BNZLYS- 1223.12170.47H-Bond
(Protein Donor)
N6OGLU- 1712.93148.3H-Bond
(Ligand Donor)
N1NALA- 1733.07159.92H-Bond
(Protein Donor)