NPASS Compound

Natural Product: NPC516754

Natural Product ID	NPC516754
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(1~{S},2~{R},4~{R},7~{E},11~{E},14~{S},15~{R})-14-hydroxy-4,8,12-trimethyl-16-methylene-3,18-dioxatricyclo[13.3.0.0^{2,4}]octadeca-7,11-dien-17-one
IUPAC Name	(1~{S},2~{R},4~{R},7~{E},11~{E},14~{S},15~{R})-14-hydroxy-4,8,12-trimethyl-16-methylene-3,18-dioxatricyclo[13.3.0.0^{2,4}]octadeca-7,11-dien-17-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 52 54 0 0 0 0 0 0 0 0999 V2000 -4.3833 2.2540 -0.3775 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7896 1.0749 -0.2974 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4141 -0.2397 -0.2174 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6473 -0.4898 -0.2368 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3859 -1.1811 -0.1142 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2877 -0.6516 -0.7868 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3216 0.8345 -0.2652 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4793 1.6585 -1.1282 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3527 2.4019 -1.9834 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5519 2.6473 -0.5529 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3808 2.2015 0.5056 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1241 1.8930 1.8565 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6788 2.1893 0.2672 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7415 1.7815 1.1933 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6949 0.7819 0.6839 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2976 -0.5995 0.4617 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3701 -1.5433 -0.0839 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0756 -1.1227 0.6913 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8293 -2.5680 0.4158 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7471 -2.8296 -0.5690 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6482 -2.4529 -0.1698 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6251 -3.6164 -0.2324 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7740 -1.5556 0.8844 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9529 -1.1588 -0.5283 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.4608 2.2679 -0.3866 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8637 3.1915 -0.4296 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4642 -0.5866 -1.8926 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0462 0.8264 0.7912 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9626 0.9833 -1.8876 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7258 2.8662 -2.6172 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0408 3.0785 -1.4253 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1179 3.5720 -0.2005 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6352 2.3495 2.5827 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0643 2.4679 2.0823 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1690 0.8519 2.1313 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0552 2.5171 -0.7365 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3351 1.4297 2.1797 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2691 2.7497 1.4831 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5830 0.8118 1.3937 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1748 1.2327 -0.2520 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0943 -1.9379 -1.0599 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3040 -0.9633 -0.1868 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5817 -2.3506 0.6224 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2709 -0.5249 1.0703 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7665 -3.0308 0.0205 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5186 -3.0820 1.3644 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0019 -2.2505 -1.5173 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8200 -3.9051 -0.8779 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6162 -3.3730 0.1447 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7056 -3.9274 -1.2823 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2152 -4.5032 0.3337 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1177 -0.4702 -0.8643 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 3 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 8 10 1 0 10 11 1 0 11 12 1 0 11 13 2 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 16 18 2 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 1 21 23 1 0 23 24 1 0 7 2 1 0 24 21 1 0 24 6 1 0 1 25 1 0 1 26 1 0 6 27 1 6 7 28 1 1 8 29 1 6 9 30 1 0 10 31 1 0 10 32 1 0 12 33 1 0 12 34 1 0 12 35 1 0 13 36 1 0 14 37 1 0 14 38 1 0 15 39 1 0 15 40 1 0 17 41 1 0 17 42 1 0 17 43 1 0 18 44 1 0 19 45 1 0 19 46 1 0 20 47 1 0 20 48 1 0 22 49 1 0 22 50 1 0 22 51 1 0 24 52 1 6 M END

Standard InCHIKey	ARVXFCIVVWNIRM-CRDNPJFJSA-N
Standard InCHI	InChI=1S/C20H28O4/c1-12-7-5-8-13(2)11-15(21)16-14(3)19(22)23-17(16)18-20(4,24-18)10-6-9-12/h8-9,15-18,21H,3,5-7,10-11H2,1-2,4H3/b12-9+,13-8+/t15-,16+,17-,18+,20+/m0/s1
SMILES	C=C1C(=O)O[C@H]2[C@H]1[C@@H](O)C/C(C)=C/CC/C(C)=C/CC[C@@]1(C)O[C@H]21

Calculated Properties

Physi-Chem Properties

Molecular Weight:	332.2	Volume:	353.422 ? Van der Waals volume.
Dense:	0.94	LogP:	3.157 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.006 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.63 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	0.0	Rigid Bonds:	22.0
TPSA:	59.06 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	1.0	Rings:	3.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.319	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.008	Fsp³:	0.65
MCE-18:	52.121 ? 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:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.532	Fluc inhibitor:	0.001 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.033 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.057 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.355	Promiscuous compounds:	0.31

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.04	MDCK Permeability:	-4.936
Pgp-inhibitor:	0.969	Pgp-substrate:	0.005
PAMPA:	0.058 ? 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):	0.003
20% Bioavailability (F20%):	0.044	30% Bioavailability (F30%):	0.425
50% Bioavailability (F50%):	0.925

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.602
Plasma Protein Binding (PPB):	70.485%	Volume Distribution (VD):	-0.065
Fu:	19.896% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.003
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.005	CYP1A2-substrate:	0.014
CYP2C19-inhibitor:	0.561	CYP2C19-substrate:	0.008
CYP2C9-inhibitor:	0.283	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.37	CYP2D6-substrate:	0.055
CYP3A4-inhibitor:	0.221	CYP3A4-substrate:	0.918
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.837
HLM stability:	0.421 ? 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):

9.24

Half-life (T1/2):

1.623

ADMET: Toxicity

hERG Blockers:	0.019	hERG Blockers (10um):	0.077
Human Hepatotoxicity (H-HT):	0.581	Drug-induced Liver Injury (DILI):	0.735
AMES Toxicity:	0.179	Rat Oral Acute Toxicity:	0.072
Maximum Recommended Daily Dose:	0.189	Skin Sensitization:	0.985
Carcinogencity:	0.227	Eye Corrosion:	0.158
Eye Irritation:	0.974	Respiratory Toxicity:	0.028
Drug-induced Neurotoxicity:	0.156	Ototoxicity:	0.45
Hematotoxicity:	0.269	Drug-induced Nephrotoxicity:	0.715
Genotoxicity:	0.029	RPMI-8226 Immunitoxicity:	0.079
A549 Cytotoxicity:	0.029	Hek293 Cytotoxicity:	0.173
BCF:	1.551 ? 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:	4.225 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.962 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.342 ? 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
NPO27251	Lobophytum crassum	Species	Alcyoniidae	Eukaryota	n.a.	south china sea	n.a.	PMID[18512986]
NPO27251	Lobophytum crassum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[18973388]
NPO27251	Lobophytum crassum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9548852]
NPO27251	Lobophytum crassum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27251	Lobophytum crassum	Species	Alcyoniidae	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 NPC516754 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	17264
0.1-0.2	27504
0.2-0.3	4651
0.3-0.4	352
0.4-0.5	57
0.5-0.6	21
0.6-0.7	7
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
0.6415	Remote Similarity	NPC38468
0.6415	Remote Similarity	NPC192678
0.6415	Remote Similarity	NPC319795
0.6415	Remote Similarity	NPC50362
0.6415	Remote Similarity	NPC488056
0.6415	Remote Similarity	NPC605079
0.6316	Remote Similarity	NPC605339
0.5962	Remote Similarity	NPC167881
0.5962	Remote Similarity	NPC98557
0.5789	Remote Similarity	NPC303942
0.5789	Remote Similarity	NPC57405
0.5789	Remote Similarity	NPC608845
0.5636	Remote Similarity	NPC24417
0.5614	Remote Similarity	NPC151770
0.5484	Remote Similarity	NPC474035
0.5484	Remote Similarity	NPC81386
0.5455	Remote Similarity	NPC207188
0.5439	Remote Similarity	NPC49342
0.5439	Remote Similarity	NPC251385
0.5312	Remote Similarity	NPC288876
0.5246	Remote Similarity	NPC481908
0.5246	Remote Similarity	NPC481993
0.5238	Remote Similarity	NPC473859
0.5156	Remote Similarity	NPC70235
0.5088	Remote Similarity	NPC229825
0.5088	Remote Similarity	NPC602858
0.5079	Remote Similarity	NPC231889
0.5079	Remote Similarity	NPC475659

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC516754 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6759
0.1-0.2	2332
0.2-0.3	55
0.3-0.4	3
0.4-0.5	0
0.5-0.6	0
0.6-0.7	1
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
0.6415	Remote Similarity	NPD1733	Clinical (unspecified phase)

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