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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:

4b5d

2.200 Å

X-ray

2012-08-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Achbp
ID:I6L8L2_CAPTE
AC:I6L8L2
Organism:Capitella teleta
Reign:Eukaryota
TaxID:283909
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A58 %
B42 %


Ligand binding site composition:

B-Factor:42.106
Number of residues:25
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.758681.750

% Hydrophobic% Polar
45.0554.95
According to VolSite

Ligand :
4b5d_1 Structure
HET Code: SW4
Formula: C14H21N2O2
Molecular weight: 249.329 g/mol
DrugBank ID: -
Buried Surface Area:70.27 %
Polar Surface area: 58.96 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 2
Rings: 3
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
16.013327.434719.2214


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
C03CDLYS- 864.270Hydrophobic
C07CG1ILE- 1184.220Hydrophobic
C05CG1ILE- 1183.630Hydrophobic
C03CZPHE- 1204.160Hydrophobic
C06CD2LEU- 1264.250Hydrophobic
C11CD1ILE- 1284.110Hydrophobic
N17OTRP- 1532.87157.95H-Bond
(Ligand Donor)
C07CG1VAL- 1544.50Hydrophobic
C15CE1PHE- 1754.140Hydrophobic
C15CD2TYR- 1943.950Hydrophobic
C13SGCYS- 1973.660Hydrophobic
C18SGCYS- 1973.650Hydrophobic
O01OE2GLU- 1983.12130.36H-Bond
(Ligand Donor)
C02CGGLU- 1984.040Hydrophobic
C13CE2TYR- 2013.630Hydrophobic
N09OHOH- 20802.77179.97H-Bond
(Protein Donor)