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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:

3cne

1.990 Å

X-ray

2008-03-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Putative protease I
ID:Q8A8A4_BACTN
AC:Q8A8A4
Organism:Bacteroides thetaiotaomicron
Reign:Bacteria
TaxID:226186
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B50 %
C50 %


Ligand binding site composition:

B-Factor:27.124
Number of residues:18
Including
Standard Amino Acids: 16
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.764648.000

% Hydrophobic% Polar
42.1957.81
According to VolSite

Ligand :
3cne_1 Structure
HET Code: FMN
Formula: C17H19N4O9P
Molecular weight: 454.328 g/mol
DrugBank ID: DB03247
Buried Surface Area:34.28 %
Polar Surface area: 217.05 Å2
Number of
H-Bond Acceptors: 12
H-Bond Donors: 4
Rings: 3
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
32.75426.314835.0523


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
C3'CBASN- 1614.420Hydrophobic
C7MCH2TRP- 1644.420Hydrophobic
C7MCH2TRP- 1643.730Hydrophobic
C8MCH2TRP- 1644.310Hydrophobic
C8MCZ2TRP- 1643.930Hydrophobic
C1'CE3TRP- 1643.490Hydrophobic
C2'CE2TRP- 1644.430Hydrophobic
DuArDuArTRP- 1643.530Aromatic Face/Face
DuArDuArTRP- 1643.540Aromatic Face/Face