NPASS Compound

Natural Product: NPC162869

Natural Product ID	NPC162869
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	SGWLCEXRWADMOA-ZDUSSCGKSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3397955
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002585] O-methylated flavonoids [CHEMONTID:0002593] 8-O-methylated flavonoids

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 46 48 0 0 0 0 0 0 0 0999 V2000 7.5638 0.2484 -0.0015 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5660 -0.4691 -0.7058 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2533 -0.3844 -0.2619 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9100 0.3742 0.8353 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5876 0.4186 1.2278 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5780 -0.2571 0.5822 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9393 -1.0176 -0.5221 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2515 -1.0781 -0.9335 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1505 -0.1973 1.0218 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7770 -1.3968 1.8370 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5955 -1.8605 1.6164 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9499 -2.9518 2.1185 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5651 -1.1080 0.8391 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0684 -0.1585 -0.0419 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3027 -0.0074 -0.1072 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9479 0.5750 -0.7959 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4857 1.5317 -1.6857 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3134 2.8459 -1.2286 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3070 0.3899 -0.6974 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7961 -0.5533 0.1781 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9235 -1.2986 0.9429 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3756 -2.2571 1.8351 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1662 -0.7300 0.2679 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9011 -1.6285 -0.5131 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1919 1.1379 -1.4655 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7253 2.3697 -1.0262 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3776 1.3310 -0.1599 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5831 -0.0432 -0.3159 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5147 0.0701 1.0939 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6867 0.9295 1.3792 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3464 1.0244 2.0958 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1593 -1.5577 -1.0450 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5044 -1.6843 -1.8050 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0194 0.7027 1.6577 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4670 -2.2549 1.6415 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8765 -1.1952 2.9437 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1174 3.5057 -1.5964 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3260 3.2481 -1.5571 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3318 2.9258 -0.1145 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1634 -2.1164 2.8266 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3593 -1.9148 -1.4538 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8407 -1.1231 -0.8752 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2449 -2.5208 0.0412 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5068 3.2028 -1.7333 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3758 2.6300 0.0095 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8362 2.3030 -0.9783 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 6 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 11 13 1 0 13 14 2 0 14 15 1 0 14 16 1 0 16 17 1 0 17 18 1 0 16 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 20 23 1 0 23 24 1 0 19 25 1 0 25 26 1 0 8 3 1 0 15 9 1 0 21 13 1 0 1 27 1 0 1 28 1 0 1 29 1 0 4 30 1 0 5 31 1 0 7 32 1 0 8 33 1 0 9 34 1 1 10 35 1 0 10 36 1 0 18 37 1 0 18 38 1 0 18 39 1 0 22 40 1 0 24 41 1 0 24 42 1 0 24 43 1 0 26 44 1 0 26 45 1 0 26 46 1 0 M END

Standard InCHIKey	SGWLCEXRWADMOA-ZDUSSCGKSA-N
Standard InCHI	InChI=1S/C19H20O7/c1-22-11-7-5-10(6-8-11)13-9-12(20)14-15(21)17(23-2)19(25-4)18(24-3)16(14)26-13/h5-8,13,21H,9H2,1-4H3/t13-/m0/s1
SMILES	COc1ccc(cc1)[C@@H]1CC(=O)c2c(O1)c(OC)c(c(c2O)OC)OC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	360.12	Volume:	354.587 ? Van der Waals volume.
Dense:	1.016	LogP:	3.01 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.114 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.515 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	5.0	Rigid Bonds:	18.0
TPSA:	83.45 ? Topological Polar Surface Area.	H-Bond Acceptor:	7.0
H-Bond Donor:	1.0	Rings:	3.0
Heavy Atoms:	7.0

MedChem Properties

QED Drug-Likeness Score:	0.877	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.934	Fsp³:	0.316
MCE-18:	60.04 ? 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:	1	PAINS Alert:	0
Colloidal aggregators:	0.203	Fluc inhibitor:	0.758 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.336 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.335 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.295	Promiscuous compounds:	0.062

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.934	MDCK Permeability:	-4.747
Pgp-inhibitor:	0.789	Pgp-substrate:	0.019
PAMPA:	0.063 ? 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):	0.006
20% Bioavailability (F20%):	0.009	30% Bioavailability (F30%):	0.04
50% Bioavailability (F50%):	0.551

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.172	MRP1:	0.983
Plasma Protein Binding (PPB):	96.002%	Volume Distribution (VD):	-0.39
Fu:	3.86% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.672
OATP1B3 inhibitor:	0.986	BCRP inhibitor:	0.681
BSEP inhibitor:	0.935

ADMET: Metabolism

CYP1A2-inhibitor:	0.998	CYP1A2-substrate:	0.453
CYP2C19-inhibitor:	0.544	CYP2C19-substrate:	0.896
CYP2C9-inhibitor:	0.036	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.021	CYP2D6-substrate:	0.009
CYP3A4-inhibitor:	0.999	CYP3A4-substrate:	0.333
CYP2B6-substrate:	0.001	CYP2C8-inhibitor:	0.962
HLM stability:	0.987 ? 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):

5.317

Half-life (T1/2):

0.923

ADMET: Toxicity

hERG Blockers:	0.202	hERG Blockers (10um):	0.516
Human Hepatotoxicity (H-HT):	0.758	Drug-induced Liver Injury (DILI):	0.869
AMES Toxicity:	0.595	Rat Oral Acute Toxicity:	0.591
Maximum Recommended Daily Dose:	0.609	Skin Sensitization:	0.774
Carcinogencity:	0.594	Eye Corrosion:	0.055
Eye Irritation:	0.906	Respiratory Toxicity:	0.913
Drug-induced Neurotoxicity:	0.897	Ototoxicity:	0.412
Hematotoxicity:	0.542	Drug-induced Nephrotoxicity:	0.813
Genotoxicity:	0.575	RPMI-8226 Immunitoxicity:	0.251
A549 Cytotoxicity:	0.65	Hek293 Cytotoxicity:	0.468
BCF:	1.376 ? 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:	3.77 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.65 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.499 ? 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
NPO20278	Scutellaria indica	Species	Lamiaceae	Eukaryota	whole plant	n.a.	n.a.	PMID[25637363]
NPO20278	Scutellaria indica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20278	Scutellaria indica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20278	Scutellaria indica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20278	Scutellaria indica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20278	Scutellaria indica	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	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
NPT113	Cell line	RAW264.7	Mus musculus	IC50	=	27800.0	nM	PMID[19835393]

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 NPC162869 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	25914
0.1-0.2	20173
0.2-0.3	3260
0.3-0.4	392
0.4-0.5	92
0.5-0.6	21
0.6-0.7	4
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
0.6275	Remote Similarity	NPC6407
0.6275	Remote Similarity	NPC545184
0.6038	Remote Similarity	NPC274784
0.6038	Remote Similarity	NPC20709
0.5849	Remote Similarity	NPC20354
0.5849	Remote Similarity	NPC37392
0.5818	Remote Similarity	NPC469758
0.5818	Remote Similarity	NPC601395
0.5769	Remote Similarity	NPC188243
0.5769	Remote Similarity	NPC110228
0.5741	Remote Similarity	NPC296917
0.5741	Remote Similarity	NPC170907
0.566	Remote Similarity	NPC482487
0.5636	Remote Similarity	NPC475267
0.5536	Remote Similarity	NPC48208
0.5455	Remote Similarity	NPC156057
0.5294	Remote Similarity	NPC99854
0.5283	Remote Similarity	NPC135616
0.5273	Remote Similarity	NPC150648
0.5246	Remote Similarity	NPC95936
0.5179	Remote Similarity	NPC255106
0.5179	Remote Similarity	NPC235165
0.5179	Remote Similarity	NPC329203
0.5179	Remote Similarity	NPC222342
0.5088	Remote Similarity	NPC606248

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC162869 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4378
0.1-0.2	4619
0.2-0.3	144
0.3-0.4	5
0.4-0.5	4
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