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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:

4tqq

2.500 Å

X-ray

2014-06-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Reaction center protein L chain
ID:RCEL_RHOSH
AC:P0C0Y8
Organism:Rhodobacter sphaeroides
Reign:Bacteria
TaxID:1063
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
H4 %
L88 %
M8 %


Ligand binding site composition:

B-Factor:25.733
Number of residues:28
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.485391.500

% Hydrophobic% Polar
73.2826.72
According to VolSite

Ligand :
4tqq_1 Structure
HET Code: UQ1
Formula: C14H18O4
Molecular weight: 250.290 g/mol
DrugBank ID: DB08689
Buried Surface Area:66.89 %
Polar Surface area: 52.6 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 0
Rings: 1
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-1.6539428.3773-40.8061


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
C8CD1LEU- 1894.230Hydrophobic
CM2CBHIS- 1903.890Hydrophobic
CM2CD2LEU- 1933.320Hydrophobic
CM3CD2LEU- 1933.760Hydrophobic
CM3CBGLU- 2123.890Hydrophobic
CM5CD1PHE- 2163.690Hydrophobic
C7CE1PHE- 2163.40Hydrophobic
CM5CBSER- 2234.40Hydrophobic
CM5CG2ILE- 2243.780Hydrophobic
O4NGLY- 2252.85169.67H-Bond
(Protein Donor)
CM3CG2THR- 2264.50Hydrophobic
CM2CG1ILE- 2294.170Hydrophobic
C8CD1ILE- 2293.650Hydrophobic