NPASS Compound

Natural Product: NPC326080

Natural Product ID	NPC326080
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	CBMYJHIOYJEBSB-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	11301
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0003568] Androstane steroids [CHEMONTID:0001467] Androgens and derivatives

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 53 56 0 0 0 0 0 0 0 0999 V2000 2.0888 -1.6069 1.0576 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4722 -0.4998 0.2530 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6052 -0.7409 -1.2265 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0624 -1.1801 -1.4264 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0284 -0.1459 -0.9967 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6876 0.6235 0.2176 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2457 0.8018 0.5048 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6459 1.9713 -0.1790 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1791 2.0206 -0.2704 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5468 0.7313 -0.2646 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0967 -0.2492 0.7293 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7379 -1.4245 1.0215 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8724 -1.6985 0.1070 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6064 -0.5399 -0.4152 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9585 0.7541 0.1031 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8566 1.7518 -0.4807 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2324 1.1377 -0.2066 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9842 -0.3233 0.1163 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0230 -0.5344 1.5125 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6741 -0.5645 -1.9161 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2682 -0.7882 -0.7651 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8865 -2.5940 0.5529 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1742 -1.5436 1.1663 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5948 -1.6516 2.0472 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9471 -1.5155 -1.6123 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5351 0.2307 -1.7954 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1570 -1.3368 -2.5398 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1698 -2.1662 -0.9739 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1955 0.5544 -1.8621 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2102 0.2125 1.1317 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1386 1.6542 0.1060 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1409 0.9711 1.6172 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9914 2.8933 0.3791 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1578 2.0737 -1.1820 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0905 2.5594 -1.2257 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2716 2.6709 0.5344 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4313 0.2309 -1.2609 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1781 0.3571 1.6817 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0824 -2.3454 1.0231 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1581 -1.4127 2.0727 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4708 -2.3116 -0.7527 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5746 -2.4088 0.6294 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0689 0.7459 1.2036 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7361 1.9501 -1.5478 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8088 2.7591 0.0251 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6215 1.6093 0.7121 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9019 1.2647 -1.0741 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7488 -0.9586 -0.3498 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9035 0.3062 2.0014 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3416 -1.5717 -2.2699 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1091 0.2165 -2.4184 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7361 -0.4763 -2.2877 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6910 -0.4630 0.0701 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 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 14 20 1 0 5 21 1 0 7 2 1 0 11 2 1 0 15 10 1 0 18 14 1 0 1 22 1 0 1 23 1 0 1 24 1 0 3 25 1 0 3 26 1 0 4 27 1 0 4 28 1 0 5 29 1 0 6 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 12 39 1 0 12 40 1 0 13 41 1 0 13 42 1 0 15 43 1 0 16 44 1 0 16 45 1 0 17 46 1 0 17 47 1 0 18 48 1 0 19 49 1 0 20 50 1 0 20 51 1 0 20 52 1 0 21 53 1 0 M END

Standard InCHIKey	CBMYJHIOYJEBSB-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C19H32O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h12-17,20-21H,3-11H2,1-2H3
SMILES	CC12CCC(CC1CCC3C2CCC4(C3CCC4O)C)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	292.24	Volume:	320.535 ? Van der Waals volume.
Dense:	0.912	LogP:	3.956 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.84 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.397 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	0.0	Rigid Bonds:	20.0
TPSA:	40.46 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	2.0	Rings:	4.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.714	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.007	Fsp³:	1.0
MCE-18:	69.474 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted	GSK Rule:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.062	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.019 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.006 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.609	Promiscuous compounds:	0.018

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.573	MDCK Permeability:	-4.868
Pgp-inhibitor:	0.002	Pgp-substrate:	0.858
PAMPA:	0.96 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.651
20% Bioavailability (F20%):	0.887	30% Bioavailability (F30%):	0.963
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.207	MRP1:	0.986
Plasma Protein Binding (PPB):	68.876%	Volume Distribution (VD):	-0.098
Fu:	29.492% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.003
OATP1B3 inhibitor:	0.367	BCRP inhibitor:	0.162
BSEP inhibitor:	0.189

ADMET: Metabolism

CYP1A2-inhibitor:	0.002	CYP1A2-substrate:	0.045
CYP2C19-inhibitor:	0.887	CYP2C19-substrate:	0.513
CYP2C9-inhibitor:	0.791	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.998	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.007	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.999	CYP2C8-inhibitor:	0.259
HLM stability:	0.532 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

23.16

Half-life (T1/2):

2.469

ADMET: Toxicity

hERG Blockers:	0.189	hERG Blockers (10um):	0.662
Human Hepatotoxicity (H-HT):	0.64	Drug-induced Liver Injury (DILI):	0.09
AMES Toxicity:	0.176	Rat Oral Acute Toxicity:	0.063
Maximum Recommended Daily Dose:	0.565	Skin Sensitization:	0.128
Carcinogencity:	0.5	Eye Corrosion:	0.114
Eye Irritation:	0.816	Respiratory Toxicity:	0.757
Drug-induced Neurotoxicity:	0.153	Ototoxicity:	0.811
Hematotoxicity:	0.094	Drug-induced Nephrotoxicity:	0.071
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.027
A549 Cytotoxicity:	0.263	Hek293 Cytotoxicity:	0.24
BCF:	1.752 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	3.962 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.344 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.626 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO31003	Moschus sifanicus	Species	Moschidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO463	Moschus berezovskii	Species	Moschidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2646	Moschus moschiferus	Species	Moschidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO31003	Moschus sifanicus	Species	Moschidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2646	Moschus moschiferus	Species	Moschidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO463	Moschus berezovskii	Species	Moschidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO463	Moschus berezovskii	Species	Moschidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO31003	Moschus sifanicus	Species	Moschidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2646	Moschus moschiferus	Species	Moschidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2646	Moschus moschiferus	Species	Moschidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO463	Moschus berezovskii	Species	Moschidae	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 NPC326080 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	27568
0.1-0.2	19802
0.2-0.3	2287
0.3-0.4	141
0.4-0.5	36
0.5-0.6	12
0.6-0.7	8
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	4

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC281540
1.0	High Similarity	NPC159654
1.0	High Similarity	NPC167995
1.0	High Similarity	NPC118937
0.6818	Remote Similarity	NPC44122
0.6512	Remote Similarity	NPC114891
0.617	Remote Similarity	NPC324607
0.617	Remote Similarity	NPC321732
0.6087	Remote Similarity	NPC320549
0.6087	Remote Similarity	NPC156277
0.6087	Remote Similarity	NPC58057
0.6087	Remote Similarity	NPC151018
0.5957	Remote Similarity	NPC71460
0.5957	Remote Similarity	NPC218585
0.5833	Remote Similarity	NPC327728
0.5833	Remote Similarity	NPC6120
0.5833	Remote Similarity	NPC148174
0.5833	Remote Similarity	NPC131892
0.5833	Remote Similarity	NPC213178
0.5714	Remote Similarity	NPC254340
0.5283	Remote Similarity	NPC167702
0.5283	Remote Similarity	NPC192456
0.5283	Remote Similarity	NPC280026
0.5094	Remote Similarity	NPC477820

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC326080 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8011
0.1-0.2	1012
0.2-0.3	90
0.3-0.4	21
0.4-0.5	6
0.5-0.6	7
0.6-0.7	3
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
0.617	Remote Similarity	NPD3698	Phase 2
0.6087	Remote Similarity	NPD4808	Phase 2
0.6087	Remote Similarity	NPD4809	Phase 4
0.5833	Remote Similarity	NPD3699	Clinical (unspecified phase)
0.5833	Remote Similarity	NPD3700	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD4245	Pre-clinical
0.5714	Remote Similarity	NPD4787	Phase 1
0.5385	Remote Similarity	NPD3671	Phase 1
0.5283	Remote Similarity	NPD6113	Clinical (unspecified phase)
0.52	Remote Similarity	NPD4244	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