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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:

1sqv

2.850 Å

X-ray

2004-03-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Cytochrome b
ID:CYB_BOVIN
AC:P00157
Organism:Bos taurus
Reign:Eukaryota
TaxID:9913
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:31.076
Number of residues:30
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.851479.250

% Hydrophobic% Polar
78.8721.13
According to VolSite

Ligand :
1sqv_1 Structure
HET Code: UHD
Formula: C18H24NO3S
Molecular weight: 334.453 g/mol
DrugBank ID: DB04799
Buried Surface Area:56.6 %
Polar Surface area: 98.33 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 0
Rings: 2
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 10

Mass center Coordinates

XYZ
71.699954.5233165.981


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
C18CD2LEU- 1213.780Hydrophobic
C12CEMET- 1244.440Hydrophobic
C14CEMET- 1243.840Hydrophobic
C17CBALA- 1253.850Hydrophobic
O4OHTYR- 1312.97125.92H-Bond
(Protein Donor)
S1CBTRP- 1414.20Hydrophobic
S1CG2VAL- 1454.260Hydrophobic
C8CG1ILE- 1463.580Hydrophobic
C15CG2ILE- 1464.360Hydrophobic
C11CD1ILE- 14640Hydrophobic
C13CD1ILE- 1463.760Hydrophobic
S1CG1ILE- 2683.880Hydrophobic
C9CGPRO- 2703.940Hydrophobic
C11CGPHE- 2743.450Hydrophobic
C13CZPHE- 2744.310Hydrophobic
C9CBPHE- 2743.750Hydrophobic
C10CBALA- 2774.40Hydrophobic
C10CD1LEU- 2944.490Hydrophobic