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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:

4ix4

1.500 Å

X-ray

2013-01-24

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized protein
ID:C1EBN1_MICCC
AC:C1EBN1
Organism:Micromonas commoda
Reign:Eukaryota
TaxID:296587
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A9 %
B91 %


Ligand binding site composition:

B-Factor:20.466
Number of residues:37
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
1.254415.125

% Hydrophobic% Polar
60.9839.02
According to VolSite

Ligand :
4ix4_2 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:55.31 %
Polar Surface area: 260.7 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
32.394222.72139.21396


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
C1'CD2LEU- 1783.90Hydrophobic
C4'CBLEU- 1783.430Hydrophobic
O3BNGLY- 1813.14168.47H-Bond
(Protein Donor)
O3ANGLY- 1813.05126.37H-Bond
(Protein Donor)
C5'CBVAL- 1863.940Hydrophobic
C4'CG1VAL- 1864.490Hydrophobic
N6OALA- 2622.91139.93H-Bond
(Ligand Donor)
N1NGLU- 2642.95160.46H-Bond
(Protein Donor)
C2'CG2THR- 2684.450Hydrophobic
C2'CD1ILE- 3373.570Hydrophobic
O1BMG MG- 6022.440Metal Acceptor
O1AMG MG- 6022.250Metal Acceptor
O2AOHOH- 9522.78179.98H-Bond
(Protein Donor)