NPASS Compound

Natural Product: NPC477943

Natural Product ID	NPC477943
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Tumacone B
IUPAC Name	(8S,9S,10R,13S,14S,16R,17R)-16-hydroxy-17-[(2S)-7-hydroxy-6-methyl-3-oxoheptan-2-yl]-10,13-dimethyl-1,2,6,7,8,9,11,12,14,15,16,17-dodecahydrocyclopenta[a]phenanthren-3-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	21673933
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001445] Bile acids, alcohols and derivatives [CHEMONTID:0002194] Hydroxy bile acids, alcohols and derivatives [CHEMONTID:0000516] Dihydroxy bile acids, alcohols 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 76 0 0 0 0 0 0 0 0999 V2000 2.5002 -0.5349 1.8205 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2694 -0.1234 0.4057 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0092 0.5803 0.1028 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0374 0.8823 -1.4071 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2071 0.1520 -1.9409 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1196 0.3498 -0.8084 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2640 -0.1087 0.3883 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0352 0.4735 1.5686 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4404 -0.0128 1.6265 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2118 0.2103 0.3391 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3845 -0.3981 -0.7740 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1698 -0.2865 -2.0849 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2719 -1.3214 -1.9565 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1210 -0.9021 -0.8034 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4232 -1.0669 -0.9413 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3004 -0.6757 0.1507 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3520 -1.3499 0.3793 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9177 0.5044 0.9506 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4669 0.7950 0.9535 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5999 -0.3358 0.4379 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.6715 -1.4381 1.5052 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1765 -1.5999 0.4221 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9219 2.2373 -1.6562 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4025 0.7573 0.0208 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1664 1.8980 -0.3203 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8186 0.3021 0.0349 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7426 1.4169 -0.4030 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1771 1.0165 -0.4079 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6095 0.5964 0.9780 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4092 -0.1321 -1.3574 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0608 0.1984 -2.6607 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9464 -1.5625 1.8143 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6488 -0.5606 2.4829 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2858 0.0951 2.3326 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3169 -1.0253 -0.2786 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9928 1.5784 0.6131 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8957 0.4483 -1.9106 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4990 0.7165 -2.8637 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0078 -0.8736 -2.2300 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2881 1.4251 -0.6471 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0496 1.5804 1.3852 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5669 0.3243 2.5339 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9672 0.6281 2.3948 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4373 -1.0738 1.9416 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2110 1.3069 0.1651 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2668 -1.4741 -0.5547 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6781 0.7014 -2.1501 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5106 -0.4776 -2.9416 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8214 -1.3352 -2.9003 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8345 -2.3387 -1.7936 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8326 -1.4972 -1.8730 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5206 1.3724 0.5541 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2746 0.3740 2.0005 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2971 1.6693 0.2576 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1331 1.1526 1.9432 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3990 -1.0400 2.5021 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0140 -2.2882 1.2450 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6984 -1.8388 1.6029 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3161 -2.0573 -0.6018 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9054 -2.0966 1.0693 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8305 -1.9849 0.7382 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4920 2.6965 -0.8829 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0467 -0.0621 1.0445 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9241 -0.5035 -0.7501 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4171 1.7712 -1.3974 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6196 2.3087 0.2786 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7823 1.8986 -0.6798 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4274 -0.4654 1.1690 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0703 1.2686 1.6886 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7103 0.7577 1.0322 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5157 -0.3324 -1.3338 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8919 -1.0321 -0.9788 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7078 -0.2383 -3.2674 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 2 0 15 16 1 0 16 17 2 0 16 18 1 0 18 19 1 0 19 20 1 0 20 21 1 1 7 22 1 1 4 23 1 0 2 24 1 0 24 25 2 0 24 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 28 30 1 0 30 31 1 0 7 3 1 0 11 6 1 0 20 10 1 0 20 14 1 0 1 32 1 0 1 33 1 0 1 34 1 0 2 35 1 6 3 36 1 1 4 37 1 6 5 38 1 0 5 39 1 0 6 40 1 1 8 41 1 0 8 42 1 0 9 43 1 0 9 44 1 0 10 45 1 6 11 46 1 1 12 47 1 0 12 48 1 0 13 49 1 0 13 50 1 0 15 51 1 0 18 52 1 0 18 53 1 0 19 54 1 0 19 55 1 0 21 56 1 0 21 57 1 0 21 58 1 0 22 59 1 0 22 60 1 0 22 61 1 0 23 62 1 0 26 63 1 0 26 64 1 0 27 65 1 0 27 66 1 0 28 67 1 0 29 68 1 0 29 69 1 0 29 70 1 0 30 71 1 0 30 72 1 0 31 73 1 0 M END

Standard InCHIKey	HOQRRDCNLLTOEP-FHUFBSQRSA-N
Standard InCHI	InChI=1S/C27H42O4/c1-16(15-28)5-8-23(30)17(2)25-24(31)14-22-20-7-6-18-13-19(29)9-11-26(18,3)21(20)10-12-27(22,25)4/h13,16-17,20-22,24-25,28,31H,5-12,14-15H2,1-4H3/t16?,17-,20-,21+,22+,24-,25+,26+,27+/m1/s1
SMILES	C[C@@H]([C@H]1[C@@H](C[C@@H]2[C@@]1(CC[C@H]3[C@H]2CCC4=CC(=O)CC[C@]34C)C)O)C(=O)CCC(C)CO

Calculated Properties

Physi-Chem Properties

Molecular Weight:	430.31	Volume:	468.574 ? Van der Waals volume.
Dense:	0.918	LogP:	3.17 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.203 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.663 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	22.0
TPSA:	74.6 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	2.0	Rings:	4.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.639	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.705	Fsp³:	0.852
MCE-18:	71.68 ? 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:	0.569	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.018 ? 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:	0.287	Promiscuous compounds:	0.624

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.31	MDCK Permeability:	-5.049
Pgp-inhibitor:	0.669	Pgp-substrate:	0.004
PAMPA:	0.187 ? 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%):	0.056	30% Bioavailability (F30%):	0.172
50% Bioavailability (F50%):	0.703

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.015	MRP1:	0.575
Plasma Protein Binding (PPB):	81.289%	Volume Distribution (VD):	-0.274
Fu:	17.056% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.978
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.313
BSEP inhibitor:	0.999

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.126
CYP2C19-inhibitor:	0.46	CYP2C19-substrate:	0.016
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.01
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.578
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.999
HLM stability:	0.569 ? 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):

11.827

Half-life (T1/2):

0.901

ADMET: Toxicity

hERG Blockers:	0.087	hERG Blockers (10um):	0.497
Human Hepatotoxicity (H-HT):	0.646	Drug-induced Liver Injury (DILI):	0.187
AMES Toxicity:	0.148	Rat Oral Acute Toxicity:	0.209
Maximum Recommended Daily Dose:	0.719	Skin Sensitization:	0.966
Carcinogencity:	0.716	Eye Corrosion:	0.006
Eye Irritation:	0.463	Respiratory Toxicity:	0.8
Drug-induced Neurotoxicity:	0.224	Ototoxicity:	0.575
Hematotoxicity:	0.676	Drug-induced Nephrotoxicity:	0.303
Genotoxicity:	0.182	RPMI-8226 Immunitoxicity:	0.102
A549 Cytotoxicity:	0.137	Hek293 Cytotoxicity:	0.429
BCF:	0.581 ? 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:	3.328 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.022 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.149 ? 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
NPO33704	Solanum aphyodendron	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]

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 NPC477943 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	19028
0.1-0.2	27753
0.2-0.3	2934
0.3-0.4	91
0.4-0.5	31
0.5-0.6	20
0.6-0.7	2
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
0.6	Remote Similarity	NPC214043
0.6	Remote Similarity	NPC85774
0.597	Remote Similarity	NPC111015
0.5806	Remote Similarity	NPC237712
0.5645	Remote Similarity	NPC327115
0.55	Remote Similarity	NPC307176
0.55	Remote Similarity	NPC321874
0.5484	Remote Similarity	NPC227064
0.5484	Remote Similarity	NPC329043
0.5484	Remote Similarity	NPC58841
0.5484	Remote Similarity	NPC161423
0.5397	Remote Similarity	NPC144258
0.5238	Remote Similarity	NPC282593
0.5231	Remote Similarity	NPC249312
0.5156	Remote Similarity	NPC35734
0.5156	Remote Similarity	NPC159577
0.5156	Remote Similarity	NPC115023
0.5156	Remote Similarity	NPC602429
0.5152	Remote Similarity	NPC310010
0.5152	Remote Similarity	NPC326627
0.5082	Remote Similarity	NPC139397
0.5077	Remote Similarity	NPC149203

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC477943 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6889
0.1-0.2	2003
0.2-0.3	190
0.3-0.4	39
0.4-0.5	22
0.5-0.6	4
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
0.55	Remote Similarity	NPD4747	Phase 4
0.5484	Remote Similarity	NPD3666	Phase 4
0.5238	Remote Similarity	NPD4221	Phase 4
0.5152	Remote Similarity	NPD4753	Phase 2

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