NPASS Compound

Natural Product: NPC302347

Natural Product ID	NPC302347
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	CECREIRZLPLYDM-PIKOESSRSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	636732
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] 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 55 56 0 0 0 0 0 0 0 0999 V2000 3.2283 2.2617 0.1193 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3621 1.0695 -0.4715 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8139 -0.0804 0.2874 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2275 -1.1749 -0.6978 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8833 -0.5741 1.3166 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5419 -1.0801 0.9455 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6214 -0.1214 0.3556 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2744 1.0199 1.2435 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4047 0.9384 2.5366 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2817 2.2427 0.5526 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0572 1.6967 -0.6638 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6710 0.4040 -0.2277 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9550 0.0466 -0.9120 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9162 0.0636 -2.3970 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9884 1.0933 -0.4693 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4277 -1.2668 -0.3279 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7265 -1.6609 0.9232 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2331 -1.8390 0.6173 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6756 -0.7358 -0.1999 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3193 -1.2534 -1.5625 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0252 0.2261 0.9618 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8867 3.0799 -0.5035 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4613 2.3494 1.1624 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1425 0.9549 -1.5459 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3732 -2.1188 -0.1585 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2159 -0.8845 -1.1203 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5062 -1.2398 -1.5354 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4524 -1.3511 1.9400 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8088 0.2734 2.0811 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1349 -1.5491 1.9045 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7198 -1.9190 0.2077 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1387 0.3709 -0.5255 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7534 0.0980 3.1039 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1269 1.8313 3.1250 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4742 2.9669 0.2897 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0516 2.6442 1.2671 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3435 1.6016 -1.4991 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8086 2.4393 -0.9169 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9599 0.5526 0.8587 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6654 0.7826 -2.8451 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2760 -0.9410 -2.7693 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9501 0.3523 -2.8406 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9352 1.2977 0.6021 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9809 0.6320 -0.6822 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9305 1.9999 -1.1106 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5275 -1.2515 -0.1290 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2816 -2.0455 -1.0934 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9010 -0.9998 1.7771 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1090 -2.6615 1.2187 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7690 -2.0367 1.5808 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1875 -2.8296 0.0689 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4609 -2.0528 -1.3861 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1323 -1.7743 -2.0922 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1956 -0.5018 -2.1930 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8271 0.6539 1.8285 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 0 3 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 13 15 1 0 13 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 6 3 21 1 1 19 7 1 0 19 12 1 0 1 22 1 0 1 23 1 0 2 24 1 0 4 25 1 0 4 26 1 0 4 27 1 0 5 28 1 0 5 29 1 0 6 30 1 0 6 31 1 0 7 32 1 6 9 33 1 0 9 34 1 0 10 35 1 0 10 36 1 0 11 37 1 0 11 38 1 0 12 39 1 1 14 40 1 0 14 41 1 0 14 42 1 0 15 43 1 0 15 44 1 0 15 45 1 0 16 46 1 0 16 47 1 0 17 48 1 0 17 49 1 0 18 50 1 0 18 51 1 0 20 52 1 0 20 53 1 0 20 54 1 0 21 55 1 0 M END

Standard InCHIKey	CECREIRZLPLYDM-PIKOESSRSA-N
Standard InCHI	InChI=1S/C20H34O/c1-7-19(5,21)14-11-16-15(2)9-10-17-18(3,4)12-8-13-20(16,17)6/h7,16-17,21H,1-2,8-14H2,3-6H3/t16-,17+,19-,20-/m1/s1
SMILES	C=C[C@](C)(CC[C@@H]1C(=C)CC[C@H]2C(C)(C)CCC[C@]12C)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	290.26	Volume:	340.881 ? Van der Waals volume.
Dense:	0.852	LogP:	4.298 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.776 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.504 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	13.0
TPSA:	20.23 ? Topological Polar Surface Area.	H-Bond Acceptor:	1.0
H-Bond Donor:	1.0	Rings:	2.0
Heavy Atoms:	1.0

MedChem Properties

QED Drug-Likeness Score:	0.678	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.258	Fsp³:	0.8
MCE-18:	45.0 ? 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:	0.081	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.003 ? 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:	0.966	Promiscuous compounds:	0.341

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.537	MDCK Permeability:	-4.701
Pgp-inhibitor:	0.8	Pgp-substrate:	0.0
PAMPA:	0.026 ? 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%):	0.71	30% Bioavailability (F30%):	0.933
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.011	MRP1:	0.393
Plasma Protein Binding (PPB):	98.423%	Volume Distribution (VD):	0.279
Fu:	1.339% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.997	BCRP inhibitor:	0.98
BSEP inhibitor:	0.996

ADMET: Metabolism

CYP1A2-inhibitor:	0.819	CYP1A2-substrate:	0.057
CYP2C19-inhibitor:	0.99	CYP2C19-substrate:	0.053
CYP2C9-inhibitor:	0.126	CYP2C9-substrate:	0.115
CYP2D6-inhibitor:	0.852	CYP2D6-substrate:	0.008
CYP3A4-inhibitor:	0.895	CYP3A4-substrate:	0.998
CYP2B6-substrate:	0.93	CYP2C8-inhibitor:	0.915
HLM stability:	0.625 ? 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):

10.463

Half-life (T1/2):

0.741

ADMET: Toxicity

hERG Blockers:	0.031	hERG Blockers (10um):	0.47
Human Hepatotoxicity (H-HT):	0.394	Drug-induced Liver Injury (DILI):	0.019
AMES Toxicity:	0.075	Rat Oral Acute Toxicity:	0.259
Maximum Recommended Daily Dose:	0.803	Skin Sensitization:	0.96
Carcinogencity:	0.754	Eye Corrosion:	0.989
Eye Irritation:	0.997	Respiratory Toxicity:	0.946
Drug-induced Neurotoxicity:	0.448	Ototoxicity:	0.226
Hematotoxicity:	0.104	Drug-induced Nephrotoxicity:	0.562
Genotoxicity:	0.054	RPMI-8226 Immunitoxicity:	0.042
A549 Cytotoxicity:	0.084	Hek293 Cytotoxicity:	0.616
BCF:	2.515 ? 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:	4.699 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.904 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.687 ? 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
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[10579867]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	subterranean part	n.a.	n.a.	PMID[11374949]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[11536386]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[11975496]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[24035341]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15454	Vitex rotundifolia	Species	Lamiaceae	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 NPC302347 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	26461
0.1-0.2	20250
0.2-0.3	2689
0.3-0.4	344
0.4-0.5	73
0.5-0.6	29
0.6-0.7	8
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC41160
1.0	High Similarity	NPC67840
0.7805	Intermediate Similarity	NPC476406
0.6591	Remote Similarity	NPC482894
0.6591	Remote Similarity	NPC279434
0.6591	Remote Similarity	NPC226997
0.6444	Remote Similarity	NPC68703
0.617	Remote Similarity	NPC475077
0.6047	Remote Similarity	NPC88454
0.6047	Remote Similarity	NPC101307
0.6047	Remote Similarity	NPC117607
0.5833	Remote Similarity	NPC484730
0.5833	Remote Similarity	NPC484729
0.5818	Remote Similarity	NPC192999
0.5714	Remote Similarity	NPC484731
0.5714	Remote Similarity	NPC189745
0.5714	Remote Similarity	NPC175334
0.5686	Remote Similarity	NPC251528
0.5641	Remote Similarity	NPC103290
0.551	Remote Similarity	NPC185587
0.55	Remote Similarity	NPC476438
0.549	Remote Similarity	NPC99321
0.54	Remote Similarity	NPC35655
0.5306	Remote Similarity	NPC107258
0.5283	Remote Similarity	NPC217394
0.5283	Remote Similarity	NPC18819
0.5283	Remote Similarity	NPC46610
0.5283	Remote Similarity	NPC601249
0.5208	Remote Similarity	NPC143765
0.52	Remote Similarity	NPC169275
0.52	Remote Similarity	NPC52449
0.5185	Remote Similarity	NPC79027
0.5106	Remote Similarity	NPC64123
0.5102	Remote Similarity	NPC69649
0.5091	Remote Similarity	NPC311070
0.5091	Remote Similarity	NPC472809
0.5091	Remote Similarity	NPC177037
0.5091	Remote Similarity	NPC472810
0.5091	Remote Similarity	NPC475709
0.5091	Remote Similarity	NPC472814

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC302347 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8031
0.1-0.2	1037
0.2-0.3	72
0.3-0.4	9
0.4-0.5	0
0.5-0.6	1
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
0.5091	Remote Similarity	NPD4695	Discontinued

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