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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:

4n1g

1.500 Å

X-ray

2013-10-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Obelin
ID:OBL_OBELO
AC:Q27709
Organism:Obelia longissima
Reign:Eukaryota
TaxID:32570
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:19.755
Number of residues:43
Including
Standard Amino Acids: 42
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.880415.125

% Hydrophobic% Polar
75.6124.39
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median4n1gHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802550Highcharts.com
Ligand :
4n1g_2 Structure
HET Code: CEI
Formula: C25H21N3O3
Molecular weight: 411.453 g/mol
DrugBank ID: DB04049
Buried Surface Area:77.24 %
Polar Surface area: 95.34 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 4
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
20.50145.540651.0748
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median4n1gRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


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
O25ND1HIS- 222.73159.76H-Bond
(Ligand Donor)
C24CEMET- 253.590Hydrophobic
C21CGMET- 253.730Hydrophobic
C22CBMET- 253.360Hydrophobic
C30CEMET- 253.560Hydrophobic
C29CE2PHE- 283.020Hydrophobic
C28CD2LEU- 294.250Hydrophobic
C23CD1LEU- 293.560Hydrophobic
C26CBALA- 463.670Hydrophobic
C26CD1ILE- 503.40Hydrophobic
O25OHTYR- 882.63158.1H-Bond
(Protein Donor)
C21CZ2TRP- 923.360Hydrophobic
C26CZ2TRP- 1144.480Hydrophobic
C11CG1VAL- 1183.730Hydrophobic
C12CG2VAL- 1183.60Hydrophobic
C16CG1VAL- 1183.740Hydrophobic
C29CBSER- 1423.610Hydrophobic
C30CG2ILE- 1444.110Hydrophobic
C15CEMET- 1713.670Hydrophobic
N4NE2HIS- 1752.95176.62H-Bond
(Protein Donor)
DuArDuArHIS- 1753.720Aromatic Face/Face
C14CBHIS- 1753.620Hydrophobic
C21CE3TRP- 1793.380Hydrophobic
O33OHTYR- 1902.54161.61H-Bond
(Protein Donor)
N1OHOH- 3012.95164.79H-Bond
(Ligand Donor)