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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:

2bmc

2.600 Å

X-ray

2005-03-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Aurora kinase A
ID:AURKA_HUMAN
AC:O14965
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.1


Chains:

Chain Name:Percentage of Residues
within binding site
F100 %


Ligand binding site composition:

B-Factor:41.002
Number of residues:33
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.546516.375

% Hydrophobic% Polar
50.9849.02
According to VolSite

Ligand :
2bmc_6 Structure
HET Code: MPY
Formula: C28H33N7O2
Molecular weight: 499.607 g/mol
DrugBank ID: -
Buried Surface Area:48.15 %
Polar Surface area: 97.47 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 5
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 2
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-59.953253.032411.6884


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
C7CD2LEU- 1394.270Hydrophobic
C34CG2VAL- 1473.430Hydrophobic
O26NZLYS- 1623.13140.28H-Bond
(Protein Donor)
DuArNZLYS- 1623.7165.19Pi/Cation
N2OGLU- 2112.89154.56H-Bond
(Ligand Donor)
N4NALA- 2132.97178.5H-Bond
(Protein Donor)
N5OALA- 2133.23135.96H-Bond
(Ligand Donor)
C36CG2THR- 2174.210Hydrophobic
C36CGLEU- 2633.880Hydrophobic
C32CBALA- 2734.020Hydrophobic