NPASS Compound

Natural Product: NPC9007

Natural Product ID	NPC9007
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	SOJWLJKPIIODOH-OTWHNJEPSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	26183495
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 48 50 0 0 0 0 0 0 0 0999 V2000 5.3202 -0.6280 -0.5836 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5262 0.2507 0.3529 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9994 0.0033 1.7467 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0728 0.1042 0.1739 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5001 -1.1149 0.4668 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1464 -1.2990 0.3150 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2883 -0.2796 -0.1367 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.9307 -0.4261 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0083 2.0452 -0.9071 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3202 1.8889 -0.1976 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9053 0.5989 -0.7924 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1641 -0.5642 -0.2728 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2653 -1.7404 -1.2544 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6281 -1.0651 1.0666 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1070 -1.0228 1.2513 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8614 -0.7209 -0.0180 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3870 0.5636 -0.6046 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.8901 1.7126 0.2523 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0272 0.7131 -1.8423 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2337 1.0954 -0.2661 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2696 -0.2743 -1.6356 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0428 -1.6873 -0.4679 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3982 -0.5103 -0.2892 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7758 1.3124 0.0595 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0488 -1.1024 1.8921 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3716 0.4781 2.5149 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0271 0.4634 1.8343 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1133 -1.9535 0.8241 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7298 -2.2791 0.5573 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1789 1.9686 -1.9938 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4319 3.0371 -0.6153 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1982 1.7535 0.8938 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9476 2.7603 -0.4259 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6950 0.6695 -1.8892 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9304 -1.4565 -2.1222 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2889 -1.9755 -1.7257 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7000 -2.6333 -0.7774 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2989 -2.1287 1.1547 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1143 -0.5098 1.8682 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3792 -0.2221 1.9892 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5339 -1.9699 1.6662 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8492 -1.5762 -0.6929 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9328 -0.5860 0.2923 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2318 1.9508 1.0862 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0754 2.6098 -0.3811 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8866 1.4028 0.6410 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0199 1.6795 -2.0805 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6463 2.0507 -0.5011 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 6 12 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 17 19 1 6 8 20 2 0 20 4 1 0 12 7 1 0 17 11 1 0 1 21 1 0 1 22 1 0 1 23 1 0 2 24 1 0 3 25 1 0 3 26 1 0 3 27 1 0 5 28 1 0 6 29 1 0 9 30 1 0 9 31 1 0 10 32 1 0 10 33 1 0 11 34 1 6 13 35 1 0 13 36 1 0 13 37 1 0 14 38 1 0 14 39 1 0 15 40 1 0 15 41 1 0 16 42 1 0 16 43 1 0 18 44 1 0 18 45 1 0 18 46 1 0 19 47 1 0 20 48 1 0 M END

Standard InCHIKey	SOJWLJKPIIODOH-OTWHNJEPSA-N
Standard InCHI	InChI=1S/C19H28O/c1-13(2)14-6-8-16-15(12-14)7-9-17-18(16,3)10-5-11-19(17,4)20/h6,8,12-13,17,20H,5,7,9-11H2,1-4H3/t17-,18+,19-/m0/s1
SMILES	CC(C)c1ccc2c(CC[C@H]3[C@]2(C)CCC[C@]3(C)O)c1

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO3762	Amentotaxus argotaenia	Species	Taxaceae	Eukaryota	Leaves; Twigs	n.a.	n.a.	PMID[32633512]
NPO822	Cressa cretica	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11832	Pinus banksiana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4144	Scutia buxifolia	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1191	Castanea mollissima	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3102	Arachniodes exilis	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9522	Pericopsis angolensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9311	Parkia clappertoniana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9051	Delesseria sanguinea	Species	Delesseriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1191	Castanea mollissima	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4144	Scutia buxifolia	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4144	Scutia buxifolia	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1191	Castanea mollissima	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12322	Amomum krervanh	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9522	Pericopsis angolensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3102	Arachniodes exilis	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1191	Castanea mollissima	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12322	Amomum krervanh	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11832	Pinus banksiana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12895	Polypodiodes niponica	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1191	Castanea mollissima	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10177	Eria linearifolia	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9522	Pericopsis angolensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9051	Delesseria sanguinea	Species	Delesseriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10588	Diploschistes violarius	Species	Graphidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4144	Scutia buxifolia	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9311	Parkia clappertoniana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5205	Gymnoascus reesii	Species	Gymnoascaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12322	Amomum krervanh	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3762	Amentotaxus argotaenia	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO822	Cressa cretica	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3102	Arachniodes exilis	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC9007 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	28932
0.1-0.2	20388
0.2-0.3	438
0.3-0.4	71
0.4-0.5	20
0.5-0.6	10
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.5849	Remote Similarity	NPC220596
0.5686	Remote Similarity	NPC249018
0.5577	Remote Similarity	NPC3190
0.5556	Remote Similarity	NPC60408
0.5536	Remote Similarity	NPC225079
0.5517	Remote Similarity	NPC480861
0.5472	Remote Similarity	NPC324602
0.537	Remote Similarity	NPC125226
0.5357	Remote Similarity	NPC128248
0.5357	Remote Similarity	NPC136810

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC9007 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5737
0.1-0.2	3349
0.2-0.3	62
0.3-0.4	2
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data