NPASS Compound

Natural Product: NPC91014

Natural Product ID	NPC91014
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	HJGNLNQZLLETFV-FWQKHDEFSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	11320871
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal glycosides

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

Chemical Representations

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Standard InCHIKey	HJGNLNQZLLETFV-FWQKHDEFSA-N
Standard InCHI	InChI=1S/C70H116O38/c1-24(6-7-25(2)30-10-11-31-29-9-8-27-16-28(12-14-69(27,4)32(29)13-15-70(30,31)5)96-63-51(88)44(81)40(77)33(17-71)97-63)26(3)61(94)108-68-60(47(84)43(80)39(103-68)23-95-62-54(91)48(85)57(36(20-74)100-62)104-64-52(89)45(82)41(78)34(18-72)98-64)107-67-56(93)50(87)59(38(22-76)102-67)106-66-55(92)49(86)58(37(21-75)101-66)105-65-53(90)46(83)42(79)35(19-73)99-65/h8,24-26,28-60,62-68,71-93H,6-7,9-23H2,1-5H3/t24-,25-,26+,28+,29+,30-,31+,32+,33-,34-,35-,36-,37-,38-,39-,40-,41-,42-,43-,44+,45+,46+,47+,48-,49-,50-,51-,52-,53-,54-,55-,56-,57-,58-,59-,60-,62-,63-,64+,65+,66+,67+,68+,69+,70-/m1/s1
SMILES	C[C@H](CC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)[C@H](C)C(=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)O)O)O1)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1564.71	Volume:	1453.91 ? Van der Waals volume.
Dense:	1.076	LogP:	-0.576 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.286 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.679 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	27.0	Rigid Bonds:	63.0
TPSA:	611.58 ? Topological Polar Surface Area.	H-Bond Acceptor:	38.0
H-Bond Donor:	23.0	Rings:	11.0
Heavy Atoms:	38.0

MedChem Properties

QED Drug-Likeness Score:	0.028	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.004	Fsp³:	0.957
MCE-18:	229.314 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.673	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.001 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.493	Promiscuous compounds:	0.024

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-8.063	MDCK Permeability:	-4.878
Pgp-inhibitor:	0.0	Pgp-substrate:	0.515
PAMPA:	1.0 ? 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):	0.999
20% Bioavailability (F20%):	0.01	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.0
Plasma Protein Binding (PPB):	16.381%	Volume Distribution (VD):	-0.312
Fu:	61.57% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.003	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.735
HLM stability:	0.0 ? 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):

-2.166

Half-life (T1/2):

5.674

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	0.0
Human Hepatotoxicity (H-HT):	0.848	Drug-induced Liver Injury (DILI):	0.999
AMES Toxicity:	1.0	Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.0	Skin Sensitization:	1.0
Carcinogencity:	0.004	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.923	Drug-induced Nephrotoxicity:	0.998
Genotoxicity:	0.148	RPMI-8226 Immunitoxicity:	0.439
A549 Cytotoxicity:	0.999	Hek293 Cytotoxicity:	0.743
BCF:	1.09 ? 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:	3.36 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.671 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.527 ? 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
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[10230514]
NPO13332	Tacca chantrieri	Species	Taccaceae	Eukaryota	rhizomes	SiMao City, Yunnan Province, China	1996-OCT	PMID[11908966]
NPO13332	Tacca chantrieri	Species	Taccaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[12350150]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12956064]
NPO12186	Oplopanax chironium	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15104479]
NPO11157	Corydalis saxicola	Species	Papaveraceae	Eukaryota	n.a.	root	n.a.	PMID[17611928]
NPO11157	Corydalis saxicola	Species	Papaveraceae	Eukaryota	n.a.	leaf	n.a.	PMID[18649321]
NPO13332	Tacca chantrieri	Species	Taccaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20715765]
NPO7143	Acacia jacquemontii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21894904]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25608854]
NPO13332	Tacca chantrieri	Species	Taccaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33253561]
NPO1133	Zieria laevigata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13332	Tacca chantrieri	Species	Taccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12268	Aloe littoralis	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11396	Metzgeria furcata	Species	Metzgeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO6266	Anzia hypoleucoides	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8399	Psiadia trinervia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14634	Artemisia balchanorum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11157	Corydalis saxicola	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12093	Papaver orientale	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10695	Pelargonium zonale	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13831	Cephalotaxus oliveri	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13426	Lemmaphyllum microphyllum	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12093	Papaver orientale	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13831	Cephalotaxus oliveri	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10695	Pelargonium zonale	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13332	Tacca chantrieri	Species	Taccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13426	Lemmaphyllum microphyllum	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10695	Pelargonium zonale	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO13527	Solanum ecuadorense	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3227	Androsace umbellata	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10094	Daphne gnidioides	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13426	Lemmaphyllum microphyllum	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6266	Anzia hypoleucoides	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13332	Tacca chantrieri	Species	Taccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12268	Aloe littoralis	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14308	Coleonema pulchrum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14018	Pleurotus salmoneostramineus	Species	Pleurotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13831	Cephalotaxus oliveri	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9487	Penicillium flexuosum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12093	Papaver orientale	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8399	Psiadia trinervia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7143	Acacia jacquemontii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14634	Artemisia balchanorum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11753	Sideroxylon foetidissimum	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5551	Podocarpus sylvestris	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11396	Metzgeria furcata	Species	Metzgeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1133	Zieria laevigata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11157	Corydalis saxicola	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11909	Othonna arborescens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9126	Stevia maimarensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11585	Geijera salicifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10695	Pelargonium zonale	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13723	Salvia eriophora	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12186	Oplopanax chironium	Species	Araliaceae	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 NPC91014 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	20198
0.1-0.2	24492
0.2-0.3	3714
0.3-0.4	1238
0.4-0.5	185
0.5-0.6	26
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	Natural Product ID
0.6458	Remote Similarity	NPC486114
0.6196	Remote Similarity	NPC22140
0.6196	Remote Similarity	NPC243728
0.5766	Remote Similarity	NPC477809
0.5684	Remote Similarity	NPC21064
0.5631	Remote Similarity	NPC272015
0.5567	Remote Similarity	NPC282669
0.5521	Remote Similarity	NPC158088
0.5481	Remote Similarity	NPC295389
0.5439	Remote Similarity	NPC6806
0.5259	Remote Similarity	NPC475182
0.5254	Remote Similarity	NPC475550
0.5207	Remote Similarity	NPC23808
0.5207	Remote Similarity	NPC87998
0.5175	Remote Similarity	NPC486388
0.5158	Remote Similarity	NPC207617
0.5158	Remote Similarity	NPC607440
0.5126	Remote Similarity	NPC247037
0.5122	Remote Similarity	NPC308140
0.5089	Remote Similarity	NPC470432
0.5089	Remote Similarity	NPC230507
0.5089	Remote Similarity	NPC306991
0.5089	Remote Similarity	NPC94272
0.5085	Remote Similarity	NPC73243
0.5085	Remote Similarity	NPC244086
0.5085	Remote Similarity	NPC84956
0.5043	Remote Similarity	NPC249553
0.5043	Remote Similarity	NPC98696
0.5041	Remote Similarity	NPC477811

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC91014 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6969
0.1-0.2	2030
0.2-0.3	137
0.3-0.4	11
0.4-0.5	3
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