NPASS Compound

Natural Product: NPC319002

Natural Product ID	NPC319002
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	VZHQDHQAMFXIJW-CGTZTZSPSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	6431532
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001194] Oxosteroids [CHEMONTID:0003058] 20-oxosteroids

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 50 53 0 0 0 0 0 0 0 0999 V2000 2.5566 0.4861 1.8696 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0587 0.2443 0.4386 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1020 1.3473 0.1335 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2339 1.1191 0.7658 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6899 -0.2993 0.7305 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0811 -1.1733 -0.1978 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5276 -1.1294 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4487 -1.9126 -0.6020 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7640 -1.1376 -0.5166 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2414 0.3038 -0.5083 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3166 1.1729 0.0120 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6684 2.1374 -0.6230 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1035 -0.9207 -1.6378 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1659 0.0124 -2.0464 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1504 0.3728 -1.0163 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0287 1.3167 -1.3026 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0445 1.7425 -0.3443 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7413 2.7868 -0.5083 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2572 0.9209 0.8508 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9548 0.3494 1.3402 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1402 -0.3051 0.2783 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6521 -1.7117 0.0841 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4168 -0.1660 2.0687 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6823 0.2692 2.5227 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7688 1.5658 1.9697 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5258 2.2809 0.6117 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0372 1.5952 -0.9464 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1900 1.4476 1.8395 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9668 1.8245 0.2870 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6797 -0.7686 1.7362 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2509 -2.2349 0.0126 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5287 -1.6244 1.2745 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1319 -2.0825 -1.6254 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6704 -2.9304 -0.1657 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3735 -1.3139 -1.4164 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2795 -1.2959 0.4307 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9356 0.5919 -1.5341 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7893 0.9561 0.9499 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2490 -1.8848 -2.2129 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8767 -0.5310 -2.0471 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7644 -0.3755 -2.9244 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7441 0.9867 -2.4349 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0166 1.8048 -2.2688 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0244 0.1269 0.6710 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6719 1.5289 1.7055 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1848 -0.4420 2.1125 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3873 1.1325 1.8766 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5499 -2.3445 0.9759 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2008 -2.2120 -0.7930 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7384 -1.6272 -0.1333 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 6 13 1 0 13 14 1 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 17 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 7 2 1 0 10 2 1 0 21 5 1 0 21 15 1 0 1 23 1 0 1 24 1 0 1 25 1 0 3 26 1 0 3 27 1 0 4 28 1 0 4 29 1 0 5 30 1 0 6 31 1 0 7 32 1 0 8 33 1 0 8 34 1 0 9 35 1 0 9 36 1 0 10 37 1 0 11 38 1 0 13 39 1 0 13 40 1 0 14 41 1 0 14 42 1 0 16 43 1 0 19 44 1 0 19 45 1 0 20 46 1 0 20 47 1 0 22 48 1 0 22 49 1 0 22 50 1 0 M END

Standard InCHIKey	VZHQDHQAMFXIJW-CGTZTZSPSA-N
Standard InCHI	InChI=1S/C20H28O2/c1-19-9-7-15(22)11-13(19)3-5-16-17-6-4-14(12-21)20(17,2)10-8-18(16)19/h11-12,14,16-18H,3-10H2,1-2H3/t14-,16?,17?,18?,19+,20-/m1/s1
SMILES	CC12CCC3C(C1CCC2C=O)CCC4=CC(=O)CCC34C

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
NPO20902	Atractylodes macrocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17432574]
NPO20902	Atractylodes macrocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20902	Atractylodes macrocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20902	Atractylodes macrocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20902	Atractylodes macrocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20902	Atractylodes macrocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20902	Atractylodes macrocephala	Species	Asteraceae	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 NPC319002 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	20981
0.1-0.2	25904
0.2-0.3	2785
0.3-0.4	127
0.4-0.5	28
0.5-0.6	17
0.6-0.7	8
0.7-0.8	1
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
0.7609	Intermediate Similarity	NPC307176
0.7609	Intermediate Similarity	NPC321874
0.7143	Intermediate Similarity	NPC214043
0.7143	Intermediate Similarity	NPC85774
0.7143	Intermediate Similarity	NPC282593
0.7	Intermediate Similarity	NPC35734
0.7	Intermediate Similarity	NPC159577
0.7	Intermediate Similarity	NPC115023
0.7	Intermediate Similarity	NPC602429
0.6863	Remote Similarity	NPC149203
0.6863	Remote Similarity	NPC237712
0.6731	Remote Similarity	NPC249312
0.6327	Remote Similarity	NPC139397
0.614	Remote Similarity	NPC320514
0.6078	Remote Similarity	NPC2634
0.6078	Remote Similarity	NPC265782
0.6078	Remote Similarity	NPC251929
0.5849	Remote Similarity	NPC227064
0.5849	Remote Similarity	NPC329043
0.5849	Remote Similarity	NPC58841
0.5849	Remote Similarity	NPC161423
0.5818	Remote Similarity	NPC323765
0.5741	Remote Similarity	NPC144258
0.5741	Remote Similarity	NPC327115
0.5439	Remote Similarity	NPC310010
0.5439	Remote Similarity	NPC326627
0.5397	Remote Similarity	NPC187159
0.5357	Remote Similarity	NPC328539
0.5263	Remote Similarity	NPC303613
0.5246	Remote Similarity	NPC305039
0.5246	Remote Similarity	NPC205860
0.5085	Remote Similarity	NPC185936
0.5085	Remote Similarity	NPC168027
0.5085	Remote Similarity	NPC469948

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC319002 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6245
0.1-0.2	2646
0.2-0.3	170
0.3-0.4	57
0.4-0.5	12
0.5-0.6	15
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

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7609	Intermediate Similarity	NPD4747	Phase 4
0.6481	Remote Similarity	NPD5737	Phase 4
0.625	Remote Similarity	NPD6672	Phase 4
0.6078	Remote Similarity	NPD4691	Approved
0.5849	Remote Similarity	NPD3666	Phase 4
0.5849	Remote Similarity	NPD4221	Phase 4
0.5714	Remote Similarity	NPD5330	Phase 4
0.5536	Remote Similarity	NPD4693	Phase 3
0.5517	Remote Similarity	NPD6409	Approved
0.5439	Remote Similarity	NPD4753	Phase 2
0.5246	Remote Similarity	NPD6083	Phase 4
0.5246	Remote Similarity	NPD6084	Phase 2
0.5246	Remote Similarity	NPD6684	Phase 4
0.5246	Remote Similarity	NPD6904	Phase 4
0.5246	Remote Similarity	NPD7334	Approved
0.5246	Remote Similarity	NPD7521	Phase 4
0.5172	Remote Similarity	NPD6938	Clinical (unspecified phase)
0.5172	Remote Similarity	NPD6939	Phase 3
0.5161	Remote Similarity	NPD6903	Phase 4

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