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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:

3seq

2.730 Å

X-ray

2011-06-10

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glutamine-dependent NAD(+) synthetase
ID:NADE_MYCTU
AC:P9WJJ3
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:6.3.5.1


Chains:

Chain Name:Percentage of Residues
within binding site
A40 %
D60 %


Ligand binding site composition:

B-Factor:40.187
Number of residues:44
Including
Standard Amino Acids: 41
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.626641.250

% Hydrophobic% Polar
37.8962.11
According to VolSite

Ligand :
3seq_4 Structure
HET Code: NXX
Formula: C21H24N6O15P2
Molecular weight: 662.394 g/mol
DrugBank ID: -
Buried Surface Area:55.15 %
Polar Surface area: 340.58 Å2
Number of
H-Bond Acceptors: 19
H-Bond Donors: 5
Rings: 5
Aromatic rings: 3
Anionic atoms: 3
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 11

Mass center Coordinates

XYZ
-1.2707-64.252869.8742


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
N1ANH1ARG- 3543.15134.69H-Bond
(Protein Donor)
C5NCBALA- 4594.020Hydrophobic
O1AND2ASN- 4713.2165.36H-Bond
(Protein Donor)
O3BOGLY- 4753.09171.62H-Bond
(Ligand Donor)
C1BCG2ILE- 4764.040Hydrophobic
C5NCBTHR- 4923.880Hydrophobic
O2ANTYR- 4932.63157.4H-Bond
(Protein Donor)
C5BCZPHE- 6344.280Hydrophobic
C1BCZPHE- 6344.260Hydrophobic
DuArDuArPHE- 6343.610Aromatic Face/Face
O2ANZLYS- 6353125.62H-Bond
(Protein Donor)
O2ANZLYS- 63530Ionic
(Protein Cationic)
N6AOSER- 6613.26149.51H-Bond
(Ligand Donor)