NPASS Compound

Natural Product: NPC26959

Natural Product ID	NPC26959
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Gelliusterol B
IUPAC Name	(3S,8S,9S,10R,13R,14S,17R)-17-[(2R)-hex-4-yn-2-yl]-3-hydroxy-10,13-dimethyl-1,2,3,4,8,9,11,12,14,15,16,17-dodecahydrocyclopenta[a]phenanthren-7-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL460037
PubChem CID	11046848
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001194] 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 63 66 0 0 0 0 0 0 0 0999 V2000 7.4057 2.5328 0.9969 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6715 1.6303 0.8161 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8349 0.5677 0.5950 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9264 -0.6053 0.3286 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5908 0.0116 -0.0866 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5235 -1.0286 -0.3580 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3613 -1.8960 0.9171 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4258 -0.9383 1.6999 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3938 -0.8812 0.6583 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1612 -0.4618 -0.5870 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1345 1.0087 -0.8544 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3468 -1.1148 -1.6906 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0445 -0.5871 -1.6684 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7202 -0.5398 -0.3462 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8354 -0.1160 0.8083 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5536 -0.4043 2.0885 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9911 -0.8462 3.0812 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0088 -0.1215 2.0880 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6406 0.1343 0.9911 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0226 0.1817 -0.3483 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9259 1.6369 -0.7659 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0122 -0.4649 -1.3253 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9858 -1.3443 -0.5327 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9302 -0.3581 0.1622 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1171 0.3997 1.1559 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4417 0.5440 -0.7671 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9153 0.6744 -1.4490 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2505 3.2949 1.9199 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5610 2.3001 1.2330 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5368 3.3627 0.1832 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8809 -1.0989 1.3207 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4121 -1.1902 -0.4404 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3369 0.7548 0.6683 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8477 -1.6726 -1.1814 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7098 -2.7367 0.6133 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2569 -2.1486 1.4153 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9853 -0.0313 1.8947 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1032 -1.4653 2.6169 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0898 -1.9674 0.4598 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6367 1.6423 -0.1348 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0833 1.3610 -0.9155 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4660 1.1298 -1.9322 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2691 -2.2142 -1.4259 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7940 -1.0538 -2.6802 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1439 0.3803 -2.2359 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6241 -1.3190 -2.3217 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9844 -1.6233 -0.1076 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6888 0.9888 0.8462 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4643 -0.1589 3.0673 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0036 2.1305 -0.4785 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7235 2.1783 -0.1761 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2357 1.7658 -1.8257 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6235 0.3529 -1.7444 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5273 -0.9739 -2.1238 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5963 -1.9112 -1.2451 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5049 -1.9250 0.2504 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7531 -0.8764 0.6915 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4678 0.1884 2.1769 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2097 1.5006 0.9640 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3065 0.9154 -0.4976 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5184 0.0837 -2.2915 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0298 0.6946 -1.6237 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6275 1.7281 -1.4125 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 3 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 6 10 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 2 0 16 18 1 0 18 19 2 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 24 26 1 0 5 27 1 0 10 6 1 0 20 14 1 0 15 9 1 0 25 19 1 0 1 28 1 0 1 29 1 0 1 30 1 0 4 31 1 0 4 32 1 0 5 33 1 1 6 34 1 6 7 35 1 0 7 36 1 0 8 37 1 0 8 38 1 0 9 39 1 6 11 40 1 0 11 41 1 0 11 42 1 0 12 43 1 0 12 44 1 0 13 45 1 0 13 46 1 0 14 47 1 1 15 48 1 6 18 49 1 0 21 50 1 0 21 51 1 0 21 52 1 0 22 53 1 0 22 54 1 0 23 55 1 0 23 56 1 0 24 57 1 1 25 58 1 0 25 59 1 0 26 60 1 0 27 61 1 0 27 62 1 0 27 63 1 0 M END

Standard InCHIKey	HHGLFNRDPUBPSI-GBWULGRTSA-N
Standard InCHI	InChI=1S/C25H36O2/c1-5-6-7-16(2)19-8-9-20-23-21(11-13-25(19,20)4)24(3)12-10-18(26)14-17(24)15-22(23)27/h15-16,18-21,23,26H,7-14H2,1-4H3/t16-,18+,19-,20+,21+,23+,24+,25-/m1/s1
SMILES	CC#CC[C@H]([C@H]1CC[C@@H]2[C@]1(C)CC[C@H]1[C@H]2C(=O)C=C2[C@]1(C)CC[C@@H](C2)O)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	368.27	Volume:	413.765 ? Van der Waals volume.
Dense:	0.89	LogP:	3.916 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.596 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.577 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	2.0	Rigid Bonds:	22.0
TPSA:	37.3 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	1.0	Rings:	4.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.684	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.605	Fsp³:	0.8
MCE-18:	68.178 ? 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:	0.754	Fluc inhibitor:	0.011 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.011 ? 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:	0.294	Promiscuous compounds:	0.312

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.274	MDCK Permeability:	-5.044
Pgp-inhibitor:	0.603	Pgp-substrate:	0.01
PAMPA:	0.25 ? 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%):	0.049	30% Bioavailability (F30%):	0.505
50% Bioavailability (F50%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005	MRP1:	0.036
Plasma Protein Binding (PPB):	86.827%	Volume Distribution (VD):	-0.094
Fu:	8.257% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.98
BSEP inhibitor:	0.987

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.001	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.243
CYP2D6-inhibitor:	0.035	CYP2D6-substrate:	0.363
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.39
HLM stability:	0.097 ? 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):

16.216

Half-life (T1/2):

1.382

ADMET: Toxicity

hERG Blockers:	0.083	hERG Blockers (10um):	0.233
Human Hepatotoxicity (H-HT):	0.686	Drug-induced Liver Injury (DILI):	0.932
AMES Toxicity:	0.253	Rat Oral Acute Toxicity:	0.123
Maximum Recommended Daily Dose:	0.733	Skin Sensitization:	0.958
Carcinogencity:	0.91	Eye Corrosion:	0.434
Eye Irritation:	0.98	Respiratory Toxicity:	0.921
Drug-induced Neurotoxicity:	0.101	Ototoxicity:	0.497
Hematotoxicity:	0.423	Drug-induced Nephrotoxicity:	0.461
Genotoxicity:	0.177	RPMI-8226 Immunitoxicity:	0.038
A549 Cytotoxicity:	0.177	Hek293 Cytotoxicity:	0.714
BCF:	1.897 ? 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:	3.957 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.251 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.71 ? 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
NPO33338	gellius sp.	Species	Chalinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[11421735]

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

Activity Type	# Activity
IC50	5

Activity Type	# Activity
Cell line	5

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
NPT168	Cell line	P388	Mus musculus	IC50	>	1.0	ug.mL-1	DrugMatrix in vitro pharmacology data
NPT139	Cell line	HT-29	Homo sapiens	IC50	>	1.0	ug.mL-1	DrugMatrix in vitro pharmacology data
NPT81	Cell line	A549	Homo sapiens	IC50	>	1.0	ug.mL-1	DOI[10.6019/CHEMBL1201861]
NPT90	Cell line	DU-145	Homo sapiens	IC50	>	1.0	ug.mL-1	PMID[8699183]
NPT170	Cell line	SK-MEL-28	Homo sapiens	IC50	>	1.0	ug.mL-1	PMID[8699183]

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 NPC26959 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	16011
0.1-0.2	28542
0.2-0.3	4999
0.3-0.4	222
0.4-0.5	51
0.5-0.6	20
0.6-0.7	4
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9038	High Similarity	NPC268406
0.7778	Intermediate Similarity	NPC31564
0.7778	Intermediate Similarity	NPC145879
0.7321	Intermediate Similarity	NPC474778
0.7321	Intermediate Similarity	NPC474733
0.6897	Remote Similarity	NPC474732
0.6897	Remote Similarity	NPC58063
0.6885	Remote Similarity	NPC599942
0.6316	Remote Similarity	NPC189972
0.5968	Remote Similarity	NPC186688
0.5672	Remote Similarity	NPC489072
0.5424	Remote Similarity	NPC162742
0.5424	Remote Similarity	NPC304309
0.5424	Remote Similarity	NPC470228
0.5397	Remote Similarity	NPC472265
0.5397	Remote Similarity	NPC59453
0.5333	Remote Similarity	NPC221758
0.5333	Remote Similarity	NPC34019
0.5167	Remote Similarity	NPC81306
0.5161	Remote Similarity	NPC230301
0.5161	Remote Similarity	NPC198968
0.5161	Remote Similarity	NPC285893
0.5156	Remote Similarity	NPC33913
0.5082	Remote Similarity	NPC22105
0.5082	Remote Similarity	NPC107059
0.5079	Remote Similarity	NPC51014
0.5077	Remote Similarity	NPC474752
0.5077	Remote Similarity	NPC474683
0.5077	Remote Similarity	NPC603646

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC26959 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5921
0.1-0.2	2971
0.2-0.3	227
0.3-0.4	26
0.4-0.5	2
0.5-0.6	2
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
0.5333	Remote Similarity	NPD4786	Phase 1
0.5161	Remote Similarity	NPD7339	Approved

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