NPASS Compound

Natural Product: NPC479030

Natural Product ID	NPC479030
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	LOWXQBCGBQLZGC-URTHSMGSSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	10767010
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000253] Stilbenes [CHEMONTID:0000142] Stilbene glycosides

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 64 66 0 0 0 0 0 0 0 0999 V2000 3.5779 6.1727 0.6939 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6821 4.7658 0.8037 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5395 3.9841 0.6014 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3374 4.5796 0.3011 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1896 3.8571 0.0938 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1969 2.4573 0.1817 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0336 1.7247 -0.0434 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2651 0.4608 -0.0178 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5812 -0.0959 -0.2723 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6964 0.6258 -0.5588 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9528 0.0555 -0.7992 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0549 -1.3178 -0.7396 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9507 -2.1109 -0.4512 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7454 -1.4864 -0.2252 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0952 -3.4900 -0.4007 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9493 -4.2661 -0.1043 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2876 -1.9143 -0.9731 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6207 -2.2757 -2.3139 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0705 0.8101 -1.0883 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0120 2.2139 -1.1592 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4215 1.8594 0.4871 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5816 2.6117 0.6952 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4635 0.5183 0.5791 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5654 -0.2661 0.8694 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3045 -1.2408 2.0074 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8362 -2.6055 1.7943 C 0 0 2 0 0 0 0 0 0 0 0 0 4.0329 -2.6834 0.8908 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0681 -1.5835 -0.1364 C 0 0 1 0 0 0 0 0 0 0 0 0 4.5342 -2.0644 -1.4906 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5061 -0.9781 -2.3644 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7726 -1.0889 -0.2639 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2162 -2.6531 1.6174 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8229 -3.4737 1.3255 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7984 -0.6472 3.1862 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8829 6.5843 1.4829 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5451 6.6651 0.8682 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1022 6.4835 -0.2769 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2947 5.6605 0.2250 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7504 4.3566 -0.1429 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9118 2.3617 -0.2740 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4523 -0.2102 0.2003 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6823 1.6907 -0.6195 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8534 -2.0894 0.0056 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2572 -5.3180 0.1525 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4054 -3.8971 0.7911 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2264 -4.2537 -0.9435 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6215 -2.7451 -2.3461 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7011 -1.3452 -2.9456 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8481 -2.8977 -2.7775 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4810 2.5914 -2.0518 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4613 2.6228 -0.2680 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0294 2.6704 -1.0955 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5260 2.1457 0.9308 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5182 0.2395 1.0428 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2023 -1.2883 2.1271 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1409 -3.0276 2.7793 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0063 -3.6541 0.3490 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6899 -0.7728 0.2752 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5751 -2.4353 -1.4555 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8181 -2.8212 -1.8496 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9888 -0.1942 -1.9850 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9853 -2.6603 1.0198 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9343 -3.6383 0.3450 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3395 -1.2784 3.7115 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 2 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 13 15 1 0 15 16 1 0 12 17 1 0 17 18 1 0 11 19 1 0 19 20 1 0 6 21 1 0 21 22 2 0 21 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 28 31 1 0 27 32 1 0 26 33 1 0 25 34 1 0 22 3 1 0 31 24 1 0 14 9 1 0 1 35 1 0 1 36 1 0 1 37 1 0 4 38 1 0 5 39 1 0 7 40 1 0 8 41 1 0 10 42 1 0 14 43 1 0 16 44 1 0 16 45 1 0 16 46 1 0 18 47 1 0 18 48 1 0 18 49 1 0 20 50 1 0 20 51 1 0 20 52 1 0 22 53 1 0 24 54 1 1 25 55 1 1 26 56 1 1 27 57 1 6 28 58 1 1 29 59 1 0 29 60 1 0 30 61 1 0 32 62 1 0 33 63 1 0 34 64 1 0 M END

Standard InCHIKey	LOWXQBCGBQLZGC-URTHSMGSSA-N
Standard InCHI	InChI=1S/C24H30O10/c1-29-15-8-7-14(6-5-13-9-17(30-2)23(32-4)18(10-13)31-3)16(11-15)33-24-22(28)21(27)20(26)19(12-25)34-24/h5-11,19-22,24-28H,12H2,1-4H3/b6-5+/t19-,20-,21+,22-,24-/m1/s1
SMILES	COc1ccc(/C=C/c2cc(c(c(c2)OC)OC)OC)c(c1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	478.18	Volume:	467.438 ? Van der Waals volume.
Dense:	1.023	LogP:	2.378 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.527 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.958 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	9.0	Rigid Bonds:	19.0
TPSA:	136.3 ? Topological Polar Surface Area.	H-Bond Acceptor:	10.0
H-Bond Donor:	4.0	Rings:	3.0
Heavy Atoms:	10.0

MedChem Properties

QED Drug-Likeness Score:	0.388	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.689	Fsp³:	0.417
MCE-18:	69.176 ? 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:	0.499	Fluc inhibitor:	0.99 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.342 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.568 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.21	Promiscuous compounds:	0.105

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.43	MDCK Permeability:	-5.01
Pgp-inhibitor:	0.01	Pgp-substrate:	0.006
PAMPA:	0.175 ? 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):	0.044
20% Bioavailability (F20%):	0.186	30% Bioavailability (F30%):	0.893
50% Bioavailability (F50%):	0.954

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.135	MRP1:	0.15
Plasma Protein Binding (PPB):	82.201%	Volume Distribution (VD):	-0.249
Fu:	18.919% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.901
BSEP inhibitor:	0.497

ADMET: Metabolism

CYP1A2-inhibitor:	0.026	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.236	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.026	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.266	CYP2D6-substrate:	0.003
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.001
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.585 ? 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):

2.788

Half-life (T1/2):

2.974

ADMET: Toxicity

hERG Blockers:	0.149	hERG Blockers (10um):	0.223
Human Hepatotoxicity (H-HT):	0.797	Drug-induced Liver Injury (DILI):	0.952
AMES Toxicity:	0.89	Rat Oral Acute Toxicity:	0.049
Maximum Recommended Daily Dose:	0.12	Skin Sensitization:	0.911
Carcinogencity:	0.473	Eye Corrosion:	0.0
Eye Irritation:	0.032	Respiratory Toxicity:	0.053
Drug-induced Neurotoxicity:	0.118	Ototoxicity:	0.965
Hematotoxicity:	0.531	Drug-induced Nephrotoxicity:	0.901
Genotoxicity:	0.251	RPMI-8226 Immunitoxicity:	0.244
A549 Cytotoxicity:	0.556	Hek293 Cytotoxicity:	0.444
BCF:	1.14 ? 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:	3.487 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.536 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.326 ? 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
NPO20665	Erythrophleum lasianthum	Species	Fabaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[9392877]
NPO20665	Erythrophleum lasianthum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20665	Erythrophleum lasianthum	Species	Fabaceae	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	2

Activity Type	# Activity
Cell line	2

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
NPT20967	Cell line	Platelet	n.a.	IC50	=	124.4	ug	PMID[9392877]
NPT20967	Cell line	Platelet	n.a.	IC50	=	300.0	ug	PMID[9392877]

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 NPC479030 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	20750
0.1-0.2	24940
0.2-0.3	3257
0.3-0.4	627
0.4-0.5	211
0.5-0.6	53
0.6-0.7	6
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
0.7188	Intermediate Similarity	NPC475084
0.7167	Intermediate Similarity	NPC479029
0.6833	Remote Similarity	NPC479028
0.6833	Remote Similarity	NPC479031
0.6393	Remote Similarity	NPC218685
0.619	Remote Similarity	NPC210478
0.6129	Remote Similarity	NPC49074
0.6032	Remote Similarity	NPC162093
0.5965	Remote Similarity	NPC276195
0.5909	Remote Similarity	NPC232673
0.5862	Remote Similarity	NPC217854
0.5833	Remote Similarity	NPC299144
0.5735	Remote Similarity	NPC294166
0.5735	Remote Similarity	NPC115022
0.5692	Remote Similarity	NPC214910
0.5652	Remote Similarity	NPC604095
0.5645	Remote Similarity	NPC69513
0.5606	Remote Similarity	NPC248355
0.5588	Remote Similarity	NPC470236
0.5584	Remote Similarity	NPC93924
0.5556	Remote Similarity	NPC48863
0.5556	Remote Similarity	NPC251981
0.5556	Remote Similarity	NPC13745
0.5522	Remote Similarity	NPC55040
0.55	Remote Similarity	NPC153149
0.5484	Remote Similarity	NPC200092
0.5469	Remote Similarity	NPC215833
0.5455	Remote Similarity	NPC26080
0.5455	Remote Similarity	NPC165686
0.5441	Remote Similarity	NPC302378
0.5429	Remote Similarity	NPC37468
0.5424	Remote Similarity	NPC212729
0.5424	Remote Similarity	NPC604498
0.541	Remote Similarity	NPC25817
0.5333	Remote Similarity	NPC269242
0.5323	Remote Similarity	NPC609376
0.5312	Remote Similarity	NPC166040
0.5303	Remote Similarity	NPC472024
0.5303	Remote Similarity	NPC23084
0.5303	Remote Similarity	NPC604356
0.5294	Remote Similarity	NPC95392
0.5294	Remote Similarity	NPC84013
0.5294	Remote Similarity	NPC55715
0.5294	Remote Similarity	NPC35877
0.5294	Remote Similarity	NPC104167
0.5278	Remote Similarity	NPC98777
0.5246	Remote Similarity	NPC294470
0.5238	Remote Similarity	NPC608788
0.5211	Remote Similarity	NPC8497
0.5161	Remote Similarity	NPC152722
0.5139	Remote Similarity	NPC146803
0.5139	Remote Similarity	NPC604892
0.5079	Remote Similarity	NPC60589
0.5079	Remote Similarity	NPC469708
0.5075	Remote Similarity	NPC251102
0.5075	Remote Similarity	NPC270849
0.5075	Remote Similarity	NPC210298
0.5068	Remote Similarity	NPC210192
0.5068	Remote Similarity	NPC212770
0.5068	Remote Similarity	NPC475096
0.5067	Remote Similarity	NPC108674

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC479030 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4805
0.1-0.2	4190
0.2-0.3	136
0.3-0.4	18
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