NPASS Compound

Natural Product: NPC479245

Natural Product ID	NPC479245
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	XJFLGTFMOKFQFX-BPTVCEAPSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0003401] Villanovane, atisane, trachylobane or helvifulvane diterpenoids [CHEMONTID:0002738] Atisane diterpenoids

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 67 70 0 0 0 0 0 0 0 0999 V2000 7.9911 -0.6131 -1.3311 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4990 -0.6260 -1.0310 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8456 0.3944 -1.9527 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3929 0.4819 -1.7708 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6660 0.6708 -2.7999 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7102 0.3779 -0.5647 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2765 0.4797 -0.5426 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7389 0.3444 0.8218 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3480 1.4986 1.6474 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2546 0.5018 0.9395 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2095 1.6945 0.1549 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6249 1.9653 0.6239 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4597 0.8077 0.1837 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6334 0.9371 -1.3286 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7523 0.0529 -1.8290 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0379 -0.9515 -0.7343 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6714 -1.5289 -0.3260 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0014 -0.5283 0.6027 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5293 -0.7450 0.7498 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0790 -1.6438 -0.3820 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2607 -1.5987 2.0079 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1283 -1.3930 2.5471 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0976 -0.8777 1.5628 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1385 -1.4387 1.3770 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6655 -0.2095 0.4119 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.8723 1.0345 0.7495 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0551 0.2102 -0.0157 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7509 -0.9574 -0.3282 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8354 -1.0297 1.5300 O 0 0 0 0 0 0 0 0 0 0 0 0 8.2897 -1.5651 -1.8585 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2527 0.2070 -2.0525 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6064 -0.4786 -0.4388 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0546 -1.6231 -1.2312 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3620 -0.2936 -0.0013 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0372 0.0121 -2.9904 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3630 1.3715 -1.8742 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9402 -0.1997 -1.3148 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0344 1.5104 -0.9039 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6741 1.7398 2.5020 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3457 1.1899 1.9674 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3930 2.3678 0.9652 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0814 0.7976 2.0217 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1213 1.5831 -0.9300 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4011 2.5632 0.4995 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9852 2.8676 0.0608 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5945 2.1173 1.7102 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9499 1.9938 -1.5043 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7199 0.6748 -1.8717 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3961 -0.5647 -2.6996 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6189 0.6104 -2.1816 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7077 -1.7590 -1.0765 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8896 -2.4793 0.1946 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1525 -1.6630 -1.2887 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4636 -0.7304 1.6161 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7058 -2.5824 -0.2460 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9370 -2.0480 -0.1970 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2022 -1.2057 -1.3762 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4095 -2.6601 1.8188 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0124 -1.2677 2.7501 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0554 -0.7047 3.4422 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4787 -2.3603 3.0069 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7585 1.0651 1.8464 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3201 1.9457 0.3200 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0660 0.9608 -0.8262 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5786 0.6993 0.8414 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5377 -0.7848 -0.9155 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7651 -1.9938 1.2424 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 2 0 4 6 1 0 6 7 1 0 8 7 1 6 8 9 1 0 8 10 1 0 10 11 1 0 11 12 1 0 13 12 1 1 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 6 19 21 1 0 21 22 1 0 22 23 1 0 23 24 2 0 16 25 1 0 25 26 1 0 25 27 1 0 27 28 1 0 25 29 1 1 23 8 1 0 19 10 1 0 26 13 1 0 18 13 1 0 1 30 1 0 1 31 1 0 1 32 1 0 2 33 1 0 2 34 1 0 3 35 1 0 3 36 1 0 7 37 1 0 7 38 1 0 9 39 1 0 9 40 1 0 9 41 1 0 10 42 1 1 11 43 1 0 11 44 1 0 12 45 1 0 12 46 1 0 14 47 1 0 14 48 1 0 15 49 1 0 15 50 1 0 16 51 1 6 17 52 1 0 17 53 1 0 18 54 1 1 20 55 1 0 20 56 1 0 20 57 1 0 21 58 1 0 21 59 1 0 22 60 1 0 22 61 1 0 26 62 1 0 26 63 1 0 27 64 1 0 27 65 1 0 28 66 1 0 29 67 1 0 M END

Standard InCHIKey	XJFLGTFMOKFQFX-BPTVCEAPSA-N
Standard InCHI	InChI=1S/C24H38O5/c1-4-5-20(27)29-15-22(3)17-7-11-23-10-6-16(24(28,13-23)14-25)12-18(23)21(17,2)9-8-19(22)26/h16-18,25,28H,4-15H2,1-3H3/t16-,17-,18-,21+,22-,23+,24+/m0/s1
SMILES	CCCC(=O)OC[C@@]1(C)[C@H]2CC[C@]34CC[C@@H](C[C@H]4[C@]2(C)CCC1=O)[C@@](C3)(CO)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	406.27	Volume:	428.112 ? Van der Waals volume.
Dense:	0.949	LogP:	2.974 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.09 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.504 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	21.0
TPSA:	83.83 ? Topological Polar Surface Area.	H-Bond Acceptor:	5.0
H-Bond Donor:	2.0	Rings:	5.0
Heavy Atoms:	5.0

MedChem Properties

QED Drug-Likeness Score:	0.681	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.871	Fsp³:	0.917
MCE-18:	105.913 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.165	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.012 ? 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:	0.543	Promiscuous compounds:	0.813

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.716	MDCK Permeability:	-4.882
Pgp-inhibitor:	0.006	Pgp-substrate:	0.399
PAMPA:	0.966 ? 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):	0.012
20% Bioavailability (F20%):	0.408	30% Bioavailability (F30%):	0.232
50% Bioavailability (F50%):	0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.605	MRP1:	0.614
Plasma Protein Binding (PPB):	94.114%	Volume Distribution (VD):	-0.09
Fu:	7.842% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.976
OATP1B3 inhibitor:	0.946	BCRP inhibitor:	0.406
BSEP inhibitor:	0.991

ADMET: Metabolism

CYP1A2-inhibitor:	0.102	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.038	CYP2C19-substrate:	0.21
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.032
CYP3A4-inhibitor:	0.982	CYP3A4-substrate:	0.549
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.981
HLM stability:	0.717 ? 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):

6.095

Half-life (T1/2):

0.995

ADMET: Toxicity

hERG Blockers:	0.057	hERG Blockers (10um):	0.163
Human Hepatotoxicity (H-HT):	0.587	Drug-induced Liver Injury (DILI):	0.132
AMES Toxicity:	0.573	Rat Oral Acute Toxicity:	0.146
Maximum Recommended Daily Dose:	0.39	Skin Sensitization:	0.934
Carcinogencity:	0.933	Eye Corrosion:	0.003
Eye Irritation:	0.372	Respiratory Toxicity:	0.286
Drug-induced Neurotoxicity:	0.058	Ototoxicity:	0.641
Hematotoxicity:	0.663	Drug-induced Nephrotoxicity:	0.893
Genotoxicity:	0.152	RPMI-8226 Immunitoxicity:	0.049
A549 Cytotoxicity:	0.119	Hek293 Cytotoxicity:	0.254
BCF:	0.854 ? 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:	3.492 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.162 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.365 ? 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
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11858748]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24840014]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	Stems	n.a.	n.a.	PMID[31180680]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	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

Activity Type	# Activity
IC50	1

Activity Type	# Activity
Cell line	1

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
NPT34	Cell line	BV-2	Mus musculus	IC50	=	42400.0	nM	PMID[31180680]

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 NPC479245 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	20310
0.1-0.2	26307
0.2-0.3	3155
0.3-0.4	65
0.4-0.5	11
0.5-0.6	4
0.6-0.7	3
0.7-0.8	0
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8868	High Similarity	NPC479244
0.8491	Intermediate Similarity	NPC479254
0.7759	Intermediate Similarity	NPC479246
0.6364	Remote Similarity	NPC81759
0.6154	Remote Similarity	NPC479257
0.6094	Remote Similarity	NPC479256
0.5441	Remote Similarity	NPC479242
0.5333	Remote Similarity	NPC479255
0.5303	Remote Similarity	NPC479239
0.5085	Remote Similarity	NPC260116

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC479245 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6559
0.1-0.2	2510
0.2-0.3	81
0.3-0.4	0
0.4-0.5	0
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