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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:

3n8n

2.500 Å

X-ray

2010-05-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:3-dehydroquinate dehydratase
ID:AROQ_MYCTU
AC:P9WPX7
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:4.2.1.10


Chains:

Chain Name:Percentage of Residues
within binding site
I17 %
J83 %


Ligand binding site composition:

B-Factor:16.723
Number of residues:31
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.770604.125

% Hydrophobic% Polar
43.0256.98
According to VolSite

Ligand :
3n8n_8 Structure
HET Code: N88
Formula: C12H18NO6
Molecular weight: 272.274 g/mol
DrugBank ID: -
Buried Surface Area:65.13 %
Polar Surface area: 129.92 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 4
Rings: 1
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
-18.715229.152252.4046


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
C16CBASN- 123.680Hydrophobic
C17CD2LEU- 164.260Hydrophobic
O3NE2HIS- 812.71152.04H-Bond
(Ligand Donor)
C16CBASP- 884.110Hydrophobic
O1NSER- 1032.98134.57H-Bond
(Protein Donor)
O2NSER- 1033.33147.14H-Bond
(Protein Donor)
C2CG1VAL- 1053.680Hydrophobic
O3NH1ARG- 1123.43159.58H-Bond
(Protein Donor)