Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3nz2

2.350 Å

X-ray

2010-07-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Hexapeptide-repeat containing-acetyltransferase
ID:Q9KLB0_VIBCH
AC:Q9KLB0
Organism:Vibrio cholerae serotype O1
Reign:Bacteria
TaxID:243277
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
E67 %
F33 %


Ligand binding site composition:

B-Factor:22.817
Number of residues:43
Including
Standard Amino Acids: 43
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.7901728.000

% Hydrophobic% Polar
43.5556.45
According to VolSite

Ligand :
3nz2_5 Structure
HET Code: ACO
Formula: C23H34N7O17P3S
Molecular weight: 805.539 g/mol
DrugBank ID: -
Buried Surface Area:50.73 %
Polar Surface area: 429.68 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 20

Mass center Coordinates

XYZ
48.954839.584270.627


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
CH3CD2PHE- 814.140Hydrophobic
OND2ASN- 832.88164.21H-Bond
(Protein Donor)
C2PCD1LEU- 893.220Hydrophobic
CH3CBLEU- 1014.170Hydrophobic
C2PCGTYR- 1094.120Hydrophobic
CEPCD2LEU- 1153.880Hydrophobic
C6PCZ2TRP- 1373.640Hydrophobic
O5PNGLY- 1402.76153.3H-Bond
(Protein Donor)
CDPCBALA- 1573.980Hydrophobic
N6AOALA- 1583.11160.96H-Bond
(Ligand Donor)
O9PNALA- 1583.19165.25H-Bond
(Protein Donor)
N7AND2ASN- 1632.96128.64H-Bond
(Protein Donor)
CDPCD1LEU- 1713.860Hydrophobic
CEPCD1LEU- 1714.050Hydrophobic
C2BCGPRO- 1764.190Hydrophobic
C1BCD2LEU- 1804.080Hydrophobic
C4BCBLEU- 1804.410Hydrophobic
O4ACZARG- 1812.860Ionic
(Protein Cationic)