NPASS Compound

Natural Product: NPC306487

Natural Product ID	NPC306487
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	JQNGRAVMNACCCG-MYDCNYLUSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	10094206
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001510] Lignan lactones

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 57 60 0 0 0 0 0 0 0 0999 V2000 3.0357 -2.8641 3.2275 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3770 -1.5588 2.8670 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8362 -0.8678 1.8072 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8763 -1.3987 0.9646 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3448 -0.7006 -0.0882 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7650 0.5863 -0.3434 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7370 1.1517 0.4938 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2669 0.4267 1.5610 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2236 0.9923 2.3796 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6543 2.3109 2.1191 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2678 1.4246 -1.4651 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3727 0.7033 -2.4095 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6802 0.8967 -3.8792 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0025 -0.2531 -4.4171 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1149 -1.3141 -3.5006 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2260 -2.5216 -3.7059 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6871 -0.7728 -2.3081 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3275 -1.3261 -0.9722 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0140 -0.9270 -0.4784 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1043 -0.7850 -1.2865 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3076 -0.3977 -0.7382 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4612 -0.1448 0.6060 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3791 -0.2830 1.4286 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1658 -0.6744 0.8679 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4627 -0.0420 2.8086 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3232 -0.1996 3.5986 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6730 0.2455 1.1600 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9617 1.6361 1.2368 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4203 -0.2538 -1.5719 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3105 -0.5035 -2.9603 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3394 2.0452 -2.0927 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1714 -3.5983 2.4086 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9675 -2.8810 3.5438 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6274 -3.1714 4.1138 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5520 -2.4086 1.1710 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0632 2.1450 0.2998 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3420 2.6535 2.9301 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7507 2.9415 2.0628 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2464 2.2825 1.1919 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6613 2.2478 -0.9842 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6920 0.9539 -2.2945 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7452 0.8898 -4.1134 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1837 1.7727 -4.3170 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8126 -0.8407 -2.3944 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3771 -2.4128 -1.0036 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0024 -0.9880 -2.3392 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3226 -0.7744 1.5590 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5789 -0.0451 4.6703 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5240 0.5556 3.3502 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8311 -1.1898 3.4922 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8155 1.9695 2.2721 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0085 1.8428 0.9383 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3112 2.2304 0.5616 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3119 -0.5995 -3.4264 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8107 -1.4899 -3.1347 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7080 0.2607 -3.4599 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3219 3.0234 -2.0072 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 6 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 2 0 15 17 1 0 17 18 1 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 23 25 1 0 25 26 1 0 22 27 1 0 27 28 1 0 21 29 1 0 29 30 1 0 11 31 1 0 8 3 1 0 17 12 1 0 24 19 1 0 18 5 1 0 1 32 1 0 1 33 1 0 1 34 1 0 4 35 1 0 7 36 1 0 10 37 1 0 10 38 1 0 10 39 1 0 11 40 1 1 12 41 1 6 13 42 1 0 13 43 1 0 17 44 1 6 18 45 1 6 20 46 1 0 24 47 1 0 26 48 1 0 26 49 1 0 26 50 1 0 28 51 1 0 28 52 1 0 28 53 1 0 30 54 1 0 30 55 1 0 30 56 1 0 31 57 1 0 M END

Standard InCHIKey	JQNGRAVMNACCCG-MYDCNYLUSA-N
Standard InCHI	InChI=1S/C23H26O8/c1-26-15-8-12-13(9-16(15)27-2)21(24)14-10-31-23(25)20(14)19(12)11-6-17(28-3)22(30-5)18(7-11)29-4/h6-9,14,19-21,24H,10H2,1-5H3/t14-,19+,20-,21+/m0/s1
SMILES	COc1cc2c(cc1OC)[C@H]([C@H]1COC(=O)[C@@H]1[C@@H]2c1cc(c(c(c1)OC)OC)OC)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	430.16	Volume:	424.005 ? Van der Waals volume.
Dense:	1.015	LogP:	1.638 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.991 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.017 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	22.0
TPSA:	92.68 ? Topological Polar Surface Area.	H-Bond Acceptor:	8.0
H-Bond Donor:	1.0	Rings:	4.0
Heavy Atoms:	8.0

MedChem Properties

QED Drug-Likeness Score:	0.7	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.621	Fsp³:	0.435
MCE-18:	82.576 ? 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:	0.105	Fluc inhibitor:	0.106 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.107 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.066 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.09	Promiscuous compounds:	0.871

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.005	MDCK Permeability:	-4.706
Pgp-inhibitor:	0.034	Pgp-substrate:	0.021
PAMPA:	0.076 ? 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%):	0.006	30% Bioavailability (F30%):	0.0
50% Bioavailability (F50%):	0.042

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.378	MRP1:	0.999
Plasma Protein Binding (PPB):	88.516%	Volume Distribution (VD):	-0.104
Fu:	10.321% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.273
OATP1B3 inhibitor:	0.326	BCRP inhibitor:	0.002
BSEP inhibitor:	0.988

ADMET: Metabolism

CYP1A2-inhibitor:	0.031	CYP1A2-substrate:	0.867
CYP2C19-inhibitor:	1.0	CYP2C19-substrate:	0.836
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.703
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.646 ? 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):

7.415

Half-life (T1/2):

3.059

ADMET: Toxicity

hERG Blockers:	0.138	hERG Blockers (10um):	0.593
Human Hepatotoxicity (H-HT):	0.717	Drug-induced Liver Injury (DILI):	0.921
AMES Toxicity:	0.544	Rat Oral Acute Toxicity:	0.593
Maximum Recommended Daily Dose:	0.732	Skin Sensitization:	0.887
Carcinogencity:	0.62	Eye Corrosion:	0.001
Eye Irritation:	0.284	Respiratory Toxicity:	0.746
Drug-induced Neurotoxicity:	0.67	Ototoxicity:	0.783
Hematotoxicity:	0.87	Drug-induced Nephrotoxicity:	0.944
Genotoxicity:	0.933	RPMI-8226 Immunitoxicity:	0.399
A549 Cytotoxicity:	0.45	Hek293 Cytotoxicity:	0.413
BCF:	0.665 ? 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:	3.118 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.255 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.557 ? 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
NPO6545	Artemisia sieversiana	Species	Asteraceae	Eukaryota	Aerial Parts	n.a.	n.a.	PMID[29122483]
NPO6545	Artemisia sieversiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23382	Podophyllum emodii	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23382	Podophyllum emodii	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6545	Artemisia sieversiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23382	Podophyllum emodii	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6545	Artemisia sieversiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6545	Artemisia sieversiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6545	Artemisia sieversiana	Species	Asteraceae	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 NPC306487 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	20078
0.1-0.2	28311
0.2-0.3	1335
0.3-0.4	90
0.4-0.5	25
0.5-0.6	8
0.6-0.7	3
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8679	High Similarity	NPC237946
0.8679	High Similarity	NPC32373
0.7759	Intermediate Similarity	NPC119910
0.75	Intermediate Similarity	NPC178574
0.7	Intermediate Similarity	NPC91634
0.7	Intermediate Similarity	NPC150943
0.7	Intermediate Similarity	NPC268718
0.6833	Remote Similarity	NPC207584
0.6833	Remote Similarity	NPC19947
0.6066	Remote Similarity	NPC65591
0.5758	Remote Similarity	NPC288149
0.5484	Remote Similarity	NPC239890
0.5484	Remote Similarity	NPC209411
0.5156	Remote Similarity	NPC80230
0.5156	Remote Similarity	NPC104024
0.5156	Remote Similarity	NPC101755
0.5156	Remote Similarity	NPC304687
0.5156	Remote Similarity	NPC65574

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC306487 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4305
0.1-0.2	4752
0.2-0.3	81
0.3-0.4	8
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	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8679	High Similarity	NPD4965	Approved
0.8679	High Similarity	NPD4966	Phase 4
0.8679	High Similarity	NPD4967	Phase 2
0.6479	Remote Similarity	NPD37	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