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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:

4v3i

1.500 Å

X-ray

2014-10-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized protein
ID:Q9KN50_VIBCH
AC:Q9KN50
Organism:Vibrio cholerae serotype O1
Reign:Bacteria
TaxID:243277
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:17.509
Number of residues:17
Including
Standard Amino Acids: 17
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.219253.125

% Hydrophobic% Polar
48.0052.00
According to VolSite

Ligand :
4v3i_1 Structure
HET Code: ASP_LEU_THR_ARG_PRO
Formula: C25H45N8O8
Molecular weight: 585.674 g/mol
DrugBank ID: -
Buried Surface Area:27.99 %
Polar Surface area: 278.69 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 8
Rings: 1
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 2
Rule of Five Violation: 3
Rotatable Bonds: 17

Mass center Coordinates

XYZ
10.058137.3073-12.0182


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
CBCBALA- 924.010Hydrophobic
CD1CBALA- 923.890Hydrophobic
CG2CBALA- 924.350Hydrophobic
CBCD2TYR- 954.340Hydrophobic
CG2CBTYR- 954.130Hydrophobic
ONZLYS- 1342.86159.1H-Bond
(Protein Donor)
CG2CD1ILE- 1383.930Hydrophobic
ONH1ARG- 1412.68141.14H-Bond
(Protein Donor)
ONH2ARG- 1412.8129.74H-Bond
(Protein Donor)
CD2CBARG- 1414.350Hydrophobic
CD1CD2LEU- 1423.880Hydrophobic
CD2CD2LEU- 1424.050Hydrophobic
CD1CE1TYR- 1494.130Hydrophobic
CD2CZTYR- 1494.220Hydrophobic