NPASS Compound

Natural Product: NPC488144

Natural Product ID	NPC488144
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	FZOFIVYXNKRMRA-MEHDDEMSSA-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:0003782] Kaurane 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 2D 55 59 0 0 0 0 0 0 0 0999 V2000 -5.4322 0.7783 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0619 0.1682 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0000 -2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 -2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4000 0.6928 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0500 0.0866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4095 0.5130 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 -2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 -2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0905 -3.1111 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7395 1.4772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4791 2.9544 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1595 1.8121 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7628 0.9182 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6060 2.4100 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4095 0.5130 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 2.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5890 2.2701 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6457 -0.1034 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2500 -1.2990 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7395 -4.0753 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4095 -3.1111 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3680 -3.5823 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7605 -4.0753 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1639 -2.6798 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2271 1.3120 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6491 -0.9642 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4895 2.7762 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4028 1.1979 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8191 1.0261 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0906 -0.8235 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0722 1.9746 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8991 -2.2632 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0080 -0.4821 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7395 -4.0753 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4095 -3.1111 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7605 -4.0753 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1700 -4.5883 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1740 1.9158 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3130 1.9409 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6281 3.9186 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0548 3.3084 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1047 1.4963 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6700 1.9902 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 3.8971 0.0000 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 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 6 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 1 13 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 13 19 1 0 19 20 1 0 11 21 1 0 10 22 1 0 22 23 1 1 23 24 2 0 22 25 1 0 25 26 1 0 10 27 1 6 23 2 1 0 25 3 1 0 22 6 1 0 17 7 1 0 12 7 1 0 1 28 1 0 1 29 1 0 3 30 1 6 4 31 1 0 4 32 1 0 5 33 1 0 5 34 1 0 6 35 1 1 8 36 1 0 8 37 1 0 11 38 1 6 12 39 1 1 14 40 1 0 14 41 1 0 14 42 1 0 15 43 1 0 15 44 1 0 16 45 1 0 16 46 1 0 17 47 1 1 18 48 1 0 19 49 1 0 19 50 1 0 20 51 1 0 21 52 1 0 25 53 1 6 26 54 1 0 27 55 1 0 M END

Standard InCHIKey	FZOFIVYXNKRMRA-MEHDDEMSSA-N
Standard InCHI	InChI=1S/C20H28O7/c1-9-10-3-4-11-18-8-27-20(26,19(11,14(9)23)15(10)24)16(25)13(18)17(2,7-21)6-5-12(18)22/h10-13,15-16,21-22,24-26H,1,3-8H2,2H3/t10-,11-,12-,13+,15+,16-,17-,18+,19-,20-/m0/s1
SMILES	C=C1[C@@H]2CC[C@H]3[C@]45CO[C@@]([C@H]([C@@H]5[C@@](C)(CC[C@@H]4O)CO)O)([C@@]3(C1=O)[C@@H]2O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	380.18	Volume:	367.953 ? Van der Waals volume.
Dense:	1.033	LogP:	0.731 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.345 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.413 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	1.0	Rigid Bonds:	24.0
TPSA:	127.45 ? Topological Polar Surface Area.	H-Bond Acceptor:	7.0
H-Bond Donor:	5.0	Rings:	6.0
Heavy Atoms:	7.0

MedChem Properties

QED Drug-Likeness Score:	0.383	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.018	Fsp³:	0.85
MCE-18:	133.378 ? 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:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.153	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.021 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.001 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.169	Promiscuous compounds:	0.626

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.716	MDCK Permeability:	-4.721
Pgp-inhibitor:	0.0	Pgp-substrate:	0.872
PAMPA:	1.0 ? 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):	0.723
20% Bioavailability (F20%):	0.99	30% Bioavailability (F30%):	0.987
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.006	MRP1:	0.506
Plasma Protein Binding (PPB):	51.236%	Volume Distribution (VD):	-0.299
Fu:	50.614% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.936
OATP1B3 inhibitor:	0.981	BCRP inhibitor:	0.05
BSEP inhibitor:	0.017

ADMET: Metabolism

CYP1A2-inhibitor:	0.011	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.001	CYP2C19-substrate:	0.002
CYP2C9-inhibitor:	0.007	CYP2C9-substrate:	0.005
CYP2D6-inhibitor:	0.037	CYP2D6-substrate:	0.022
CYP3A4-inhibitor:	0.014	CYP3A4-substrate:	0.005
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.475
HLM stability:	0.03 ? 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):

4.178

Half-life (T1/2):

2.707

ADMET: Toxicity

hERG Blockers:	0.031	hERG Blockers (10um):	0.157
Human Hepatotoxicity (H-HT):	0.626	Drug-induced Liver Injury (DILI):	0.071
AMES Toxicity:	0.645	Rat Oral Acute Toxicity:	0.75
Maximum Recommended Daily Dose:	0.763	Skin Sensitization:	0.984
Carcinogencity:	0.448	Eye Corrosion:	0.0
Eye Irritation:	0.535	Respiratory Toxicity:	0.924
Drug-induced Neurotoxicity:	0.041	Ototoxicity:	0.84
Hematotoxicity:	0.284	Drug-induced Nephrotoxicity:	0.666
Genotoxicity:	0.893	RPMI-8226 Immunitoxicity:	0.2
A549 Cytotoxicity:	0.055	Hek293 Cytotoxicity:	0.291
BCF:	0.513 ? 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:	3.145 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.618 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.706 ? 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
NPO24459	Isodon pharicus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19425589]
NPO24459	Isodon pharicus	Species	Lamiaceae	Eukaryota	Aerial Parts	n.a.	n.a.	PMID[29286250]
NPO24459	Isodon pharicus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24459	Isodon pharicus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24459	Isodon pharicus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24459	Isodon pharicus	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

Activity Type	# Activity
IC50	5

Activity Type	# Activity
Cell line	5

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
NPT116	Cell line	HL-60	Homo sapiens	IC50	>	10000.0	nM	PMID[29286250]
NPT659	Cell line	SMMC-7721	Homo sapiens	IC50	>	10000.0	nM	PMID[29286250]
NPT81	Cell line	A549	Homo sapiens	IC50	>	10000.0	nM	PMID[29286250]
NPT83	Cell line	MCF7	Homo sapiens	IC50	>	10000.0	nM	PMID[29286250]
NPT660	Cell line	SW480	Homo sapiens	IC50	>	10000.0	nM	PMID[29286250]

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 NPC488144 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	19339
0.1-0.2	26549
0.2-0.3	3779
0.3-0.4	119
0.4-0.5	32
0.5-0.6	22
0.6-0.7	7
0.7-0.8	0
0.8-0.85	4
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC483202
0.8302	Intermediate Similarity	NPC55973
0.8302	Intermediate Similarity	NPC89860
0.8302	Intermediate Similarity	NPC189663
0.8302	Intermediate Similarity	NPC153234
0.7586	Intermediate Similarity	NPC488142
0.7586	Intermediate Similarity	NPC213320
0.7368	Intermediate Similarity	NPC488145
0.7321	Intermediate Similarity	NPC471461
0.678	Remote Similarity	NPC483201
0.6557	Remote Similarity	NPC488143
0.6552	Remote Similarity	NPC473348
0.625	Remote Similarity	NPC488148
0.6167	Remote Similarity	NPC475803
0.6129	Remote Similarity	NPC488156
0.6129	Remote Similarity	NPC488155
0.5938	Remote Similarity	NPC102741
0.5781	Remote Similarity	NPC471093
0.5556	Remote Similarity	NPC130511
0.5556	Remote Similarity	NPC471476
0.5556	Remote Similarity	NPC473324
0.5556	Remote Similarity	NPC307660
0.5538	Remote Similarity	NPC471244
0.5538	Remote Similarity	NPC473397
0.5522	Remote Similarity	NPC474927
0.5484	Remote Similarity	NPC30477
0.5469	Remote Similarity	NPC63244
0.5469	Remote Similarity	NPC122339
0.5397	Remote Similarity	NPC488146
0.5294	Remote Similarity	NPC471245
0.5238	Remote Similarity	NPC473352
0.5224	Remote Similarity	NPC145625
0.5167	Remote Similarity	NPC476168
0.5156	Remote Similarity	NPC309388
0.5147	Remote Similarity	NPC473410
0.5147	Remote Similarity	NPC471094
0.5147	Remote Similarity	NPC469984
0.5075	Remote Similarity	NPC488147

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC488144 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6638
0.1-0.2	2411
0.2-0.3	100
0.3-0.4	1
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