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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:

4n6b

3.000 Å

X-ray

2013-10-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized protein
ID:I1KHY6_SOYBN
AC:I1KHY6
Organism:Glycine max
Reign:Eukaryota
TaxID:3847
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A54 %
E46 %


Ligand binding site composition:

B-Factor:66.370
Number of residues:37
Including
Standard Amino Acids: 37
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.2961360.125

% Hydrophobic% Polar
53.1046.90
According to VolSite

Ligand :
4n6b_1 Structure
HET Code: COA
Formula: C21H32N7O16P3S
Molecular weight: 763.502 g/mol
DrugBank ID: DB01992
Buried Surface Area:35.89 %
Polar Surface area: 426.11 Å2
Number of
H-Bond Acceptors: 21
H-Bond Donors: 6
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 18

Mass center Coordinates

XYZ
-48.9502-40.1423-56.1074


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
S1PCG1VAL- 1744.370Hydrophobic
C6PCD1LEU- 1883.710Hydrophobic
C2PCD1LEU- 1884.440Hydrophobic
C6PCD1LEU- 2204.340Hydrophobic
O4ANZLYS- 2303.970Ionic
(Protein Cationic)
O5ANZLYS- 2303.060Ionic
(Protein Cationic)
O5ANZLYS- 2303.06165.43H-Bond
(Protein Donor)
O6ANZLYS- 2303.38121.46H-Bond
(Protein Donor)
O9PNALA- 2333.01132.66H-Bond
(Protein Donor)
C2BCD1LEU- 2384.380Hydrophobic
CDPCG2THR- 2464.320Hydrophobic