NPASS Compound

Natural Product: NPC230334

Natural Product ID	NPC230334
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	UAMAHWUELDAAIA-PDGQHHTCSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	15131232
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000253] Stilbenes

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 59 60 0 0 0 0 0 0 0 0999 V2000 6.8997 0.4418 -2.2650 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5216 1.1867 -1.0471 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3404 1.0145 -0.4962 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3395 0.0870 -1.0472 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0515 -0.9514 0.0241 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0696 -1.9581 -0.3605 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9600 -2.1643 0.2911 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5377 -1.4243 1.4922 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1576 -0.8293 1.3367 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0156 0.3071 0.5870 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2708 0.8414 0.4457 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3583 0.2236 1.0550 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6664 0.8682 0.8221 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4632 0.1942 -0.2499 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7590 0.9219 -0.3953 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8680 0.5377 0.3594 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0864 1.1737 0.2622 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1774 2.2363 -0.6335 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1148 2.6557 -1.4012 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9168 1.9821 -1.2634 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2143 -0.9196 1.8097 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9258 -1.4388 1.9401 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7140 -2.5821 2.6829 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3350 -1.5803 2.4671 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0228 -2.4846 1.9470 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7148 -1.2172 3.7770 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0922 0.9309 -0.0234 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2932 -2.8453 -1.5723 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5006 2.1374 -0.4543 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6425 -0.6493 -2.2131 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4127 0.8305 -3.1895 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0154 0.4593 -2.3645 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0515 1.5614 0.4063 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6559 -0.4667 -1.9433 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4458 0.6597 -1.3012 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0380 -1.5142 0.1508 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9176 -0.4367 0.9663 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2491 -2.9558 -0.0586 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5037 -2.1526 2.3543 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2023 -0.6268 1.8296 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3710 1.7435 -0.1512 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5540 1.9379 0.5094 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1900 0.8881 1.8033 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8932 0.3630 -1.2141 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6083 -0.8858 -0.1207 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7258 -0.3021 1.0412 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.9210 0.8503 0.8595 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.1262 2.7315 -0.7090 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2393 3.4893 -2.0833 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0889 2.3127 -1.8647 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2652 -2.6018 3.5865 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6762 -1.4228 4.0849 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0884 1.0057 -1.0345 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3447 -3.1525 -1.5614 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6776 -3.7632 -1.5199 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9941 -2.3080 -2.4966 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4777 1.6037 -0.4077 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5482 3.0277 -1.1128 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2226 2.4293 0.5814 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 3 3 4 1 0 4 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 12 21 1 0 21 22 2 0 22 23 1 0 21 24 1 0 24 25 2 0 24 26 1 0 10 27 1 0 6 28 1 0 2 29 1 0 22 9 1 0 20 15 1 0 1 30 1 0 1 31 1 0 1 32 1 0 3 33 1 0 4 34 1 0 4 35 1 0 5 36 1 0 5 37 1 0 7 38 1 0 8 39 1 0 8 40 1 0 11 41 1 0 13 42 1 0 13 43 1 0 14 44 1 0 14 45 1 0 16 46 1 0 17 47 1 0 18 48 1 0 19 49 1 0 20 50 1 0 23 51 1 0 26 52 1 0 27 53 1 0 28 54 1 0 28 55 1 0 28 56 1 0 29 57 1 0 29 58 1 0 29 59 1 0 M END

Standard InCHIKey	UAMAHWUELDAAIA-PDGQHHTCSA-N
Standard InCHI	InChI=1S/C25H30O4/c1-17(2)8-7-9-18(3)12-15-21-22(26)16-20(23(24(21)27)25(28)29)14-13-19-10-5-4-6-11-19/h4-6,8,10-12,16,26-27H,7,9,13-15H2,1-3H3,(H,28,29)/b18-12-
SMILES	CC(=CCC/C(=CCc1c(cc(CCc2ccccc2)c(c1O)C(=O)O)O)/C)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	394.21	Volume:	435.276 ? Van der Waals volume.
Dense:	0.906	LogP:	6.231 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.457 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.013 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	9.0	Rigid Bonds:	15.0
TPSA:	77.76 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	3.0	Rings:	2.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.469	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.674	Fsp³:	0.32
MCE-18:	15.0 ? 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:	1	PAINS Alert:	0
Colloidal aggregators:	0.864	Fluc inhibitor:	0.167 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.643 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.274 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.547	Promiscuous compounds:	0.08

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.052	MDCK Permeability:	-4.762
Pgp-inhibitor:	0.959	Pgp-substrate:	0.006
PAMPA:	0.48 ? 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):	0.011
20% Bioavailability (F20%):	0.632	30% Bioavailability (F30%):	0.743
50% Bioavailability (F50%):	0.937

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.01	MRP1:	0.963
Plasma Protein Binding (PPB):	98.263%	Volume Distribution (VD):	-0.3
Fu:	1.326% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.962
OATP1B3 inhibitor:	0.563	BCRP inhibitor:	0.03
BSEP inhibitor:	0.999

ADMET: Metabolism

CYP1A2-inhibitor:	0.002	CYP1A2-substrate:	0.087
CYP2C19-inhibitor:	0.443	CYP2C19-substrate:	0.164
CYP2C9-inhibitor:	0.993	CYP2C9-substrate:	0.001
CYP2D6-inhibitor:	0.028	CYP2D6-substrate:	0.722
CYP3A4-inhibitor:	0.001	CYP3A4-substrate:	0.721
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.989
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):

3.861

Half-life (T1/2):

1.06

ADMET: Toxicity

hERG Blockers:	0.189	hERG Blockers (10um):	0.487
Human Hepatotoxicity (H-HT):	0.668	Drug-induced Liver Injury (DILI):	0.2
AMES Toxicity:	0.162	Rat Oral Acute Toxicity:	0.129
Maximum Recommended Daily Dose:	0.297	Skin Sensitization:	0.977
Carcinogencity:	0.041	Eye Corrosion:	0.03
Eye Irritation:	0.921	Respiratory Toxicity:	0.928
Drug-induced Neurotoxicity:	0.151	Ototoxicity:	0.656
Hematotoxicity:	0.236	Drug-induced Nephrotoxicity:	0.767
Genotoxicity:	0.02	RPMI-8226 Immunitoxicity:	0.054
A549 Cytotoxicity:	0.266	Hek293 Cytotoxicity:	0.209
BCF:	1.88 ? 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:	4.856 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.332 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.858 ? 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
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18841906]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[28075580]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8326318]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8350086]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16886	Amorpha fruticosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16886	Amorpha fruticosa	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
MIC	8
IC50	2

Activity Type	# Activity
Cell line	2
Organism	8

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
NPT171	Cell line	MRC5	Homo sapiens	IC50	=	100000.0	nM	PMID[28075580]
NPT1970	Cell line	THP-1	Homo sapiens	IC50	=	100000.0	nM	PMID[28075580]
NPT88	Organism	Mycobacterium tuberculosis	Mycobacterium tuberculosis	MIC	>	50000.0	nM	PMID[28075580]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	100000.0	nM	PMID[28075580]
NPT175	Organism	Enterococcus faecalis	Enterococcus faecalis	MIC	=	100000.0	nM	PMID[28075580]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	MIC	=	100000.0	nM	PMID[28075580]
NPT747	Organism	Acinetobacter baumannii	Acinetobacter baumannii	MIC	>	50000.0	nM	PMID[28075580]

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 NPC230334 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	18814
0.1-0.2	28310
0.2-0.3	2402
0.3-0.4	258
0.4-0.5	46
0.5-0.6	18
0.6-0.7	7
0.7-0.8	0
0.8-0.85	0
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	NPC118919
0.7049	Intermediate Similarity	NPC37299
0.6875	Remote Similarity	NPC488439
0.6875	Remote Similarity	NPC292894
0.6866	Remote Similarity	NPC125801
0.6818	Remote Similarity	NPC488442
0.678	Remote Similarity	NPC600345
0.6667	Remote Similarity	NPC102384
0.6557	Remote Similarity	NPC180261
0.5507	Remote Similarity	NPC600452
0.5507	Remote Similarity	NPC600454
0.5507	Remote Similarity	NPC603936
0.5507	Remote Similarity	NPC606191
0.5507	Remote Similarity	NPC609757
0.5507	Remote Similarity	NPC611558
0.5469	Remote Similarity	NPC610690
0.5373	Remote Similarity	NPC163846
0.5362	Remote Similarity	NPC607326
0.5312	Remote Similarity	NPC479053
0.5303	Remote Similarity	NPC128676
0.5303	Remote Similarity	NPC477569
0.5294	Remote Similarity	NPC225173
0.5238	Remote Similarity	NPC33728
0.5238	Remote Similarity	NPC488443
0.5167	Remote Similarity	NPC481377
0.5152	Remote Similarity	NPC474890
0.5152	Remote Similarity	NPC273282

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC230334 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3269
0.1-0.2	5582
0.2-0.3	294
0.3-0.4	5
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