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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:

3nod

2.700 Å

X-ray

1998-03-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Nitric oxide synthase, inducible
ID:NOS2_MOUSE
AC:P29477
Organism:Mus musculus
Reign:Eukaryota
TaxID:10090
EC Number:1.14.13.39


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:42.654
Number of residues:19
Including
Standard Amino Acids: 17
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.3792136.375

% Hydrophobic% Polar
46.1353.87
According to VolSite

Ligand :
3nod_2 Structure
HET Code: H4B
Formula: C9H15N5O3
Molecular weight: 241.247 g/mol
DrugBank ID: DB00360
Buried Surface Area:46.57 %
Polar Surface area: 132 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 6
Rings: 2
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 2

Mass center Coordinates

XYZ
138.597117.86989.2345


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
O10OSER- 1123.07161.93H-Bond
(Ligand Donor)
C9SDMET- 1144.240Hydrophobic
O4NH2ARG- 3752.84129.29H-Bond
(Protein Donor)
N2OTRP- 4573.03170.05H-Bond
(Ligand Donor)