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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:

3s6g

2.670 Å

X-ray

2011-05-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:N-acetylglutamate kinase / N-acetylglutamate synthase
ID:Q0ASS9_MARMM
AC:Q0ASS9
Organism:Maricaulis maris
Reign:Bacteria
TaxID:394221
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B52 %
Y48 %


Ligand binding site composition:

B-Factor:69.605
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.091337.500

% Hydrophobic% Polar
47.0053.00
According to VolSite

Ligand :
3s6g_1 Structure
HET Code: COA
Formula: C21H32N7O16P3S
Molecular weight: 763.502 g/mol
DrugBank ID: DB01992
Buried Surface Area:38.95 %
Polar Surface area: 426.11 Å2
Number of
H-Bond Acceptors: 21
H-Bond Donors: 6
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 18

Mass center Coordinates

XYZ
97.480840.414372.1437


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
CDPCBASP- 4024.210Hydrophobic
CEPCBASP- 4024.010Hydrophobic
CDPCBVAL- 4054.130Hydrophobic
CCPCG1VAL- 4053.980Hydrophobic
O4ACZARG- 4073.870Ionic
(Protein Cationic)
O6ANH1ARG- 4072.97146.72H-Bond
(Protein Donor)
CCPCDARG- 4074.390Hydrophobic
CDPCZ2TRP- 4144.370Hydrophobic
OAPNE1TRP- 4142.9141.03H-Bond
(Protein Donor)
CEPCBGLU- 4174.350Hydrophobic
OAPOMET- 4183.29148.91H-Bond
(Ligand Donor)
S1PCGPRO- 4204.210Hydrophobic