NPASS Compound

Natural Product: NPC35530

Natural Product ID	NPC35530
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	KWVISVAMQJWJSZ-WUBAUXGGSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	31342
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002724] Steroidal alkaloids [CHEMONTID:0001704] Spirosolanes 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 73 78 0 0 0 0 0 0 0 0999 V2000 -6.4753 0.5210 1.8379 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5286 -0.0861 0.4657 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9339 -1.4686 0.4036 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7972 -1.5519 -0.5845 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8274 -0.4489 -0.2549 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6052 -0.5026 -1.1857 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9199 -0.0057 -2.5486 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6755 0.4318 -0.4064 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0596 0.0431 1.0166 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8351 -0.7748 1.4714 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2275 0.0332 0.8630 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6158 -0.4275 0.8521 C 0 0 2 0 0 0 0 0 0 0 0 0 2.1498 -0.8939 2.1865 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5800 -1.2407 1.9626 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2948 -0.6335 1.0352 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7256 -1.0647 0.8990 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6741 0.0832 0.8115 C 0 0 2 0 0 0 0 0 0 0 0 0 6.1539 1.2722 0.0736 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7387 1.6301 0.3834 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8135 0.4271 0.1238 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0096 0.0679 -1.3286 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4351 0.8205 0.4922 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7215 1.7178 -0.4502 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6064 1.1590 -1.2368 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2270 0.1086 -0.5956 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0161 -1.1868 -1.3365 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8159 -0.3689 0.1103 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2047 -0.6909 0.9655 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4340 0.8443 -0.2772 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.8568 0.7995 -0.5473 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5277 0.3561 2.3676 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5669 1.6411 1.7280 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3004 0.2122 2.4968 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6098 -0.1812 0.1854 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6032 -1.7379 1.4383 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6795 -2.2417 0.1238 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2024 -1.4197 -1.5939 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3044 -2.5303 -0.4543 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2583 -1.5460 -1.1253 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9455 0.4169 -2.5959 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1883 0.7717 -2.8417 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9122 -0.8625 -3.2720 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9048 1.4691 -0.6369 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1447 0.9606 1.6646 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9832 -1.7855 1.0960 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8637 -0.7176 2.5812 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1687 1.0641 1.2718 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8190 -1.2520 0.1331 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0275 -0.1154 2.9644 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5945 -1.8037 2.5390 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0095 -2.0152 2.5956 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0493 -1.7090 1.7447 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8419 -1.6973 -0.0141 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0351 0.3320 1.8296 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7819 2.1501 0.4105 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3255 1.2242 -1.0213 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6075 1.8817 1.4427 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4496 2.4869 -0.2375 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3386 -0.6986 -1.7092 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0241 1.0141 -1.9060 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0654 -0.3263 -1.4083 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5217 1.3761 1.4767 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4914 2.1315 -1.1681 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3420 2.6500 0.0663 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0121 0.8066 -2.2316 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0943 1.9955 -1.5334 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0201 -1.2470 -1.7391 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3193 -2.0847 -0.7988 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6435 -1.1115 -2.2757 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6481 -0.3561 -0.8672 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9389 1.5456 -0.8580 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1099 0.4944 -1.5616 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2384 1.8452 -0.3927 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 6 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 2 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 6 20 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 6 17 27 1 0 9 28 1 0 5 29 1 0 29 30 1 0 30 2 1 0 28 5 1 0 25 8 1 0 25 11 1 0 22 12 1 0 20 15 1 0 1 31 1 0 1 32 1 0 1 33 1 0 2 34 1 6 3 35 1 0 3 36 1 0 4 37 1 0 4 38 1 0 6 39 1 6 7 40 1 0 7 41 1 0 7 42 1 0 8 43 1 1 9 44 1 1 10 45 1 0 10 46 1 0 11 47 1 1 12 48 1 6 13 49 1 0 13 50 1 0 14 51 1 0 16 52 1 0 16 53 1 0 17 54 1 1 18 55 1 0 18 56 1 0 19 57 1 0 19 58 1 0 21 59 1 0 21 60 1 0 21 61 1 0 22 62 1 1 23 63 1 0 23 64 1 0 24 65 1 0 24 66 1 0 26 67 1 0 26 68 1 0 26 69 1 0 27 70 1 0 29 71 1 0 30 72 1 0 30 73 1 0 M END

Standard InCHIKey	KWVISVAMQJWJSZ-WUBAUXGGSA-N
Standard InCHI	InChI=1S/C27H43NO2/c1-16-7-12-27(28-15-16)17(2)24-23(30-27)14-22-20-6-5-18-13-19(29)8-10-25(18,3)21(20)9-11-26(22,24)4/h5,16-17,19-24,28-29H,6-15H2,1-4H3/t16-,17+,19+,20-,21+,22+,23+,24+,25+,26+,27?/m1/s1
SMILES	C[C@@H]1CCC2([C@@H](C)[C@H]3[C@H](C[C@H]4[C@@H]5CC=C6C[C@H](CC[C@]6(C)[C@H]5CC[C@]34C)O)O2)NC1

Calculated Properties

Physi-Chem Properties

Molecular Weight:	413.33	Volume:	450.15 ? Van der Waals volume.
Dense:	0.918	LogP:	4.815 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.179 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.942 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	0.0	Rigid Bonds:	30.0
TPSA:	41.49 ? Topological Polar Surface Area.	H-Bond Acceptor:	3.0
H-Bond Donor:	2.0	Rings:	6.0
Heavy Atoms:	3.0

MedChem Properties

QED Drug-Likeness Score:	0.53	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.394	Fsp³:	0.926
MCE-18:	137.077 ? 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:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.907	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.008 ? 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:	0.004	Promiscuous compounds:	0.092

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.143	MDCK Permeability:	-4.928
Pgp-inhibitor:	0.051	Pgp-substrate:	0.548
PAMPA:	0.113 ? 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):	0.0
20% Bioavailability (F20%):	0.005	30% Bioavailability (F30%):	0.023
50% Bioavailability (F50%):	0.848

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.866	MRP1:	0.918
Plasma Protein Binding (PPB):	61.485%	Volume Distribution (VD):	0.081
Fu:	41.77% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.999	BCRP inhibitor:	0.843
BSEP inhibitor:	0.937

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.063
CYP2D6-inhibitor:	0.018	CYP2D6-substrate:	0.001
CYP3A4-inhibitor:	0.244	CYP3A4-substrate:	0.911
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.181
HLM stability:	0.18 ? 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):

16.64

Half-life (T1/2):

1.241

ADMET: Toxicity

hERG Blockers:	0.268	hERG Blockers (10um):	0.442
Human Hepatotoxicity (H-HT):	0.585	Drug-induced Liver Injury (DILI):	0.352
AMES Toxicity:	0.347	Rat Oral Acute Toxicity:	0.31
Maximum Recommended Daily Dose:	0.913	Skin Sensitization:	0.954
Carcinogencity:	0.829	Eye Corrosion:	0.058
Eye Irritation:	0.593	Respiratory Toxicity:	0.818
Drug-induced Neurotoxicity:	0.201	Ototoxicity:	0.476
Hematotoxicity:	0.092	Drug-induced Nephrotoxicity:	0.42
Genotoxicity:	0.038	RPMI-8226 Immunitoxicity:	0.102
A549 Cytotoxicity:	0.658	Hek293 Cytotoxicity:	0.658
BCF:	1.971 ? 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:	3.673 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.939 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.419 ? 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
NPO2211	Solanum nigrum	Species	Solanaceae	Eukaryota	Whole plant	n.a.	steroidal saponins	PMID[16933867]
NPO2211	Solanum nigrum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2211	Solanum nigrum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2211	Solanum nigrum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2211	Solanum nigrum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2211	Solanum nigrum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO2211	Solanum nigrum	Species	Solanaceae	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 NPC35530 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	22660
0.1-0.2	24848
0.2-0.3	2066
0.3-0.4	204
0.4-0.5	41
0.5-0.6	23
0.6-0.7	4
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	NPC147835
1.0	High Similarity	NPC253645
1.0	High Similarity	NPC85001
1.0	High Similarity	NPC95920
0.7183	Intermediate Similarity	NPC485606
0.6286	Remote Similarity	NPC155985
0.6286	Remote Similarity	NPC601115
0.6136	Remote Similarity	NPC15249
0.6136	Remote Similarity	NPC25455
0.5775	Remote Similarity	NPC474164
0.5745	Remote Similarity	NPC122819
0.5658	Remote Similarity	NPC235126
0.5658	Remote Similarity	NPC242419
0.5625	Remote Similarity	NPC150057
0.5625	Remote Similarity	NPC147753
0.557	Remote Similarity	NPC212874
0.5513	Remote Similarity	NPC486119
0.5333	Remote Similarity	NPC176012
0.5294	Remote Similarity	NPC221758
0.5288	Remote Similarity	NPC287885
0.5256	Remote Similarity	NPC309493
0.5147	Remote Similarity	NPC162742
0.5147	Remote Similarity	NPC304309
0.5147	Remote Similarity	NPC470228
0.5143	Remote Similarity	NPC134847
0.5139	Remote Similarity	NPC33913
0.5139	Remote Similarity	NPC59453
0.5072	Remote Similarity	NPC22105
0.5072	Remote Similarity	NPC34019
0.5072	Remote Similarity	NPC107059
0.5072	Remote Similarity	NPC600590
0.507	Remote Similarity	NPC51014

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC35530 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7253
0.1-0.2	1798
0.2-0.3	86
0.3-0.4	6
0.4-0.5	2
0.5-0.6	3
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
0.5745	Remote Similarity	NPD8449	Approved
0.5625	Remote Similarity	NPD8450	Suspended
0.5294	Remote Similarity	NPD4786	Phase 1

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