NPASS Compound

Natural Product: NPC82144

Natural Product ID	NPC82144
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	VRCBYTZZZFFKEN-RBZNUJCTSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	5282148
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0000507] Isoflavonoid O-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 62 65 0 0 0 0 0 0 0 0999 V2000 11.0303 -0.5227 0.3516 C 0 0 0 0 0 0 0 0 0 0 0 0 10.1088 -1.5550 0.0739 O 0 0 0 0 0 0 0 0 0 0 0 0 8.7549 -1.2739 0.0378 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3051 -0.0016 0.2698 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9665 0.3141 0.2418 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0211 -0.6654 -0.0268 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4879 -1.9431 -0.2587 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8106 -2.2590 -0.2319 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6052 -0.3809 -0.0669 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9711 0.3926 0.8966 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6818 0.6445 0.8491 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9052 0.1885 -0.1026 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5411 0.4559 -0.1515 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2910 -0.0127 -1.1410 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2971 -0.7993 -2.1395 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6317 -1.0584 -2.0880 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4542 -0.5865 -1.0968 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8182 -0.8742 -1.0788 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3035 -1.5894 -2.0034 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1826 -1.8458 -3.1001 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6365 0.2271 -1.2256 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3821 0.9720 -0.3416 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1454 2.0937 -1.0593 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.7458 2.9507 0.0588 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.7972 2.0491 0.7208 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0298 0.8561 1.2594 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.9842 -0.0882 1.9564 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9663 -0.5685 1.0432 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9403 -1.4412 1.4555 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9487 -1.8089 2.6581 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.9793 -1.9567 0.5126 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.2359 -1.2124 0.7211 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.3155 -0.3085 1.5791 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.3678 -1.4890 -0.0250 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4062 0.1787 0.2314 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4919 2.6983 1.7089 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2856 4.1228 -0.4088 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3293 2.8256 -1.8861 O 0 0 0 0 0 0 0 0 0 0 0 0 11.0784 0.2057 -0.4799 H 0 0 0 0 0 0 0 0 0 0 0 0 10.7132 -0.0278 1.3005 H 0 0 0 0 0 0 0 0 0 0 0 0 12.0156 -1.0037 0.5635 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0274 0.7930 0.4847 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6233 1.3287 0.4279 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7750 -2.7296 -0.4713 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2071 -3.2611 -0.4117 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5657 0.7882 1.6957 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1590 1.0691 0.6526 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3276 -1.1920 -2.9448 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1908 -1.5687 -4.0696 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7746 1.3735 0.4779 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9959 1.6066 -1.5670 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9696 3.1060 0.8514 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4391 1.6855 -0.1102 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2959 1.2191 1.9909 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5557 0.4693 2.7410 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4825 -0.9438 2.4106 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6519 -1.8899 -0.5417 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1853 -3.0194 0.7467 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.9770 -0.7318 -0.3687 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3849 2.2542 1.7872 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4577 4.0392 -1.3669 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4559 2.3642 -1.9920 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 2 0 10 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 16 20 1 0 14 21 1 0 21 22 1 0 22 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 2 0 29 31 1 0 31 32 1 0 32 33 2 0 32 34 1 0 26 35 1 0 25 36 1 0 24 37 1 0 23 38 1 0 8 3 1 0 18 9 1 0 35 22 1 0 17 12 1 0 1 39 1 0 1 40 1 0 1 41 1 0 4 42 1 0 5 43 1 0 7 44 1 0 8 45 1 0 10 46 1 0 13 47 1 0 15 48 1 0 20 49 1 0 22 50 1 1 23 51 1 6 24 52 1 1 25 53 1 6 26 54 1 1 27 55 1 0 27 56 1 0 31 57 1 0 31 58 1 0 34 59 1 0 36 60 1 0 37 61 1 0 38 62 1 0 M END

Standard InCHIKey	VRCBYTZZZFFKEN-RBZNUJCTSA-N
Standard InCHI	InChI=1S/C25H24O13/c1-34-12-4-2-11(3-5-12)14-9-35-16-7-13(6-15(26)20(16)21(14)30)37-25-24(33)23(32)22(31)17(38-25)10-36-19(29)8-18(27)28/h2-7,9,17,22-26,31-33H,8,10H2,1H3,(H,27,28)/t17-,22-,23+,24-,25-/m1/s1
SMILES	COc1ccc(cc1)c1coc2cc(cc(c2c1=O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](COC(=O)CC(=O)O)O1)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	532.12	Volume:	494.639 ? Van der Waals volume.
Dense:	1.076	LogP:	0.951 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.487 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.815 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	9.0	Rigid Bonds:	26.0
TPSA:	202.42 ? Topological Polar Surface Area.	H-Bond Acceptor:	13.0
H-Bond Donor:	5.0	Rings:	4.0
Heavy Atoms:	13.0

MedChem Properties

QED Drug-Likeness Score:	0.197	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.991	Fsp³:	0.32
MCE-18:	89.182 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.444	Fluc inhibitor:	0.399 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.825 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.809 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.029	Promiscuous compounds:	0.403

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.103	MDCK Permeability:	-5.251
Pgp-inhibitor:	0.0	Pgp-substrate:	0.012
PAMPA:	0.997 ? 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):	0.662
20% Bioavailability (F20%):	0.033	30% Bioavailability (F30%):	0.698
50% Bioavailability (F50%):	0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005	MRP1:	0.108
Plasma Protein Binding (PPB):	83.533%	Volume Distribution (VD):	-0.515
Fu:	13.812% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.019
BSEP inhibitor:	0.007

ADMET: Metabolism

CYP1A2-inhibitor:	0.005	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.006	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.015
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.973
HLM stability:	0.0 ? 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):

1.123

Half-life (T1/2):

3.025

ADMET: Toxicity

hERG Blockers:	0.018	hERG Blockers (10um):	0.03
Human Hepatotoxicity (H-HT):	0.496	Drug-induced Liver Injury (DILI):	0.998
AMES Toxicity:	0.814	Rat Oral Acute Toxicity:	0.059
Maximum Recommended Daily Dose:	0.047	Skin Sensitization:	0.911
Carcinogencity:	0.263	Eye Corrosion:	0.0
Eye Irritation:	0.107	Respiratory Toxicity:	0.019
Drug-induced Neurotoxicity:	0.004	Ototoxicity:	0.926
Hematotoxicity:	0.438	Drug-induced Nephrotoxicity:	0.964
Genotoxicity:	0.969	RPMI-8226 Immunitoxicity:	0.096
A549 Cytotoxicity:	0.009	Hek293 Cytotoxicity:	0.045
BCF:	0.256 ? 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:	2.932 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.327 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.608 ? 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
NPO30303	Pueraria lobata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25679337]
NPO30303	Pueraria lobata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO30303	Pueraria lobata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30303	Pueraria lobata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]

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 NPC82144 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	16715
0.1-0.2	29854
0.2-0.3	2509
0.3-0.4	605
0.4-0.5	136
0.5-0.6	30
0.6-0.7	9
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
0.7363	Intermediate Similarity	NPC46202
0.6782	Remote Similarity	NPC73511
0.6628	Remote Similarity	NPC160515
0.6458	Remote Similarity	NPC64051
0.6421	Remote Similarity	NPC479405
0.6421	Remote Similarity	NPC303913
0.6354	Remote Similarity	NPC479404
0.6327	Remote Similarity	NPC229409
0.6105	Remote Similarity	NPC487212
0.6	Remote Similarity	NPC348541
0.5934	Remote Similarity	NPC197896
0.5934	Remote Similarity	NPC313163
0.5851	Remote Similarity	NPC610187
0.5784	Remote Similarity	NPC479766
0.5761	Remote Similarity	NPC234739
0.575	Remote Similarity	NPC116632
0.5743	Remote Similarity	NPC479403
0.5728	Remote Similarity	NPC479765
0.5596	Remote Similarity	NPC277532
0.5591	Remote Similarity	NPC487213
0.5514	Remote Similarity	NPC121703
0.5446	Remote Similarity	NPC22062
0.5446	Remote Similarity	NPC473634
0.5446	Remote Similarity	NPC475155
0.5446	Remote Similarity	NPC138811
0.5385	Remote Similarity	NPC51326
0.5377	Remote Similarity	NPC235575
0.5376	Remote Similarity	NPC45165
0.5333	Remote Similarity	NPC488089
0.5263	Remote Similarity	NPC156457
0.5258	Remote Similarity	NPC80140
0.5238	Remote Similarity	NPC473623
0.5213	Remote Similarity	NPC135345
0.514	Remote Similarity	NPC231194
0.5111	Remote Similarity	NPC249824
0.5111	Remote Similarity	NPC133400
0.5054	Remote Similarity	NPC25547
0.5052	Remote Similarity	NPC181712
0.5051	Remote Similarity	NPC43761
0.505	Remote Similarity	NPC211594

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC82144 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3446
0.1-0.2	5586
0.2-0.3	106
0.3-0.4	8
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