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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:

5ii2

2.100 Å

X-ray

2016-03-01

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Protein polybromo-1
ID:PB1_HUMAN
AC:Q86U86
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A22 %
B78 %


Ligand binding site composition:

B-Factor:21.304
Number of residues:29
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.4981204.875

% Hydrophobic% Polar
59.9440.06
According to VolSite

Ligand :
5ii2_2 Structure
HET Code: LU2
Formula: C15H9O6
Molecular weight: 285.228 g/mol
DrugBank ID: -
Buried Surface Area:70.4 %
Polar Surface area: 110.05 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
9.15524-23.727-28.6408


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
C13CD1ILE- 6834.220Hydrophobic
C13CD1ILE- 6833.90Hydrophobic
C15CG1ILE- 6833.350Hydrophobic
O1OPHE- 6842.69140.54H-Bond
(Ligand Donor)
C2CBPHE- 6844.40Hydrophobic
C3CD2LEU- 6873.560Hydrophobic
C15CGPRO- 6883.60Hydrophobic
C10CD1LEU- 6934.40Hydrophobic
C11CD2LEU- 6934.110Hydrophobic
O2OHTYR- 6962.6148.29H-Bond
(Protein Donor)
C2CBASP- 7054.30Hydrophobic
C3CGMET- 7313.960Hydrophobic
C4CBALA- 7353.910Hydrophobic
O3ND2ASN- 7393.08145.66H-Bond
(Protein Donor)
C14CD2LEU- 7443.660Hydrophobic
C11CD1ILE- 7453.880Hydrophobic