NPASS Natural Product

Natural Product: NPC120926

Natural Product ID:	NPC120926
Common Name:	Germacrene D
IUPAC Name:	(1E,6E,8S)-1-methyl-5-methylidene-8-propan-2-ylcyclodeca-1,6-diene
Synonyms:	Germacrene D
Molecular Formula:	C15H24
Standard InCHIKey:	GAIBLDCXCZKKJE-RXJOXMPGSA-N
Standard InCHI:	InChI=1S/C15H24/c1-12(2)15-10-8-13(3)6-5-7-14(4)9-11-15/h7-8,10,12,15H,3,5-6,9,11H2,1-2,4H3/b10-8+,14-7+/t15-/m0/s1
Canonical SMILES:	C/C/1=CCCC(=C)/C=C/[C@@H](CC1)C(C)C
First Find Year:
Max Developmental Stage:
Synthetic Gene Cluster:	;

Species Source

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Reference
NPO10001	Gnidia subcordata	Species	Thymelaeaceae	Eukaryota	UNPD*
NPO10082	Citrus unshiu	Species	Rutaceae	Eukaryota	TM-MC*
NPO10114	Micromonospora rosaria	Species	Micromonosporaceae	Bacteria	UNPD*
NPO10163	Oreoherzogia fallax	Species	Rhamnaceae	Eukaryota	UNPD*
NPO10309	Ichthyothere terminalis	Species	Asteraceae	Eukaryota	UNPD*
NPO10310	Cutaneotrichosporon cutaneum	Species	Trichosporonaceae	Eukaryota	UNPD*
NPO10328	Sida hermaphrodita	Species	Malvaceae	Eukaryota	UNPD*
NPO10330	Streptomyces coelicolor	Species	Streptomycetaceae	Bacteria	StreptomeDB*
NPO10343	Piper clusii	Species	Piperaceae	Eukaryota	UNPD*
NPO10402	Strophanthus eminii	Species	Apocynaceae	Eukaryota	UNPD*

Showing 1 to 10 of 339 entries

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Biological Activity

Activity Type	# Activity
IC50	2
Others	5

Activity Type	# Activity
Organism	6
Tissue	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	7.5	%	10560729
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	1.6	%	10560729
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	16.7	%	10560729
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	29	%	10560729
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	68.5	%	10560729
NPT32	Organism	Mus musculus	Mus musculus	IC50	=	58000	nM	10560729
NPT548	Tissue	Ileum	Cavia porcellus	IC50	=	1490	nM	16933870

Showing 1 to 7 of 7 entries

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Similar Natural Products in NPASS

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC120926 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	271
0.1-0.2	4450
0.2-0.3	16280
0.3-0.4	7245
0.4-0.5	2082
0.5-0.6	449
0.6-0.7	73
0.7-0.8	29
0.8-0.85	5
0.85-0.9	3
0.9-0.95	1
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.56	Remote Similarity	NPC15162
0.561	Remote Similarity	NPC179103
0.561	Remote Similarity	NPC76765
0.5614	Remote Similarity	NPC123194
0.5614	Remote Similarity	NPC223604

Showing 1 to 5 of 200 entries

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Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC120926 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	268
0.1-0.2	3818
0.2-0.3	3797
0.3-0.4	999
0.4-0.5	250
0.5-0.6	25
0.6-0.7	3
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.6071	Remote Similarity	NPD4219	Approved
0.6739	Remote Similarity	NPD1799	Clinical (unspecified phase)
0.6939	Remote Similarity	NPD8262	Approved
0.7561	Intermediate Similarity	NPD319	Phase 1

Showing 1 to 4 of 4 entries

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Structure

External Identifiers

PubChem CID	5317570
ChEMBL	CHEMBL105432
ZINC

Physicochemical Properties

Molecular Weight:	204.19
ALogP:	2.7967
MLogP:	3.11
XLogP:	6.294
# Rotatable Bonds:	4
Polar Surface Area:	0
# H-Bond Aceptor:	0
# H-Bond Donor:	0
# Rings:	1
# Heavy Atoms:	15

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