NPASS Compound

Natural Product: NPC480698

Natural Product ID	NPC480698
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	HZUKVQHPHZPOEM-PLVUCCGMSA-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:0000261] Phenylpropanoids and polyketides [CHEMONTID:0003405] 2-arylbenzofuran 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 76 78 0 0 0 0 0 0 0 0999 V2000 8.9238 1.4094 0.8224 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5558 0.0273 0.3537 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4110 -0.9099 1.5324 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2870 0.0348 -0.5008 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1215 0.5656 0.2474 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4896 -0.1354 1.0768 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7174 1.8724 0.0260 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6145 2.3888 0.7116 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3403 1.7435 0.3290 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2251 0.7956 -0.5655 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9693 0.1483 -0.9492 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7513 0.4752 -0.4032 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4251 -0.1624 -0.7929 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8372 -0.0030 -0.3630 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3904 1.2214 -1.0610 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7415 1.4358 -0.6950 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5233 2.4611 -1.1473 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0356 3.2945 -1.9496 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9385 2.6507 -0.7388 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9353 3.7043 0.3787 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3478 4.9602 -0.1897 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3339 3.9111 0.9235 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5277 -1.2126 -0.8977 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6033 -2.3174 0.1013 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5068 -3.0542 0.5050 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6347 -4.0695 1.4452 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8421 -4.3913 2.0163 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9548 -3.6569 1.6183 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8083 -2.6515 0.6826 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1722 -3.9592 2.1745 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3762 -3.3242 1.8883 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9873 -5.4039 2.9581 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7174 -1.6350 -1.9649 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4379 -1.1502 -1.7405 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8015 -1.4916 -2.3041 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9503 -0.8519 -1.9070 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8339 -2.4861 -3.2666 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0036 -2.9132 -3.8996 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0164 1.5234 0.6686 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6996 1.5075 1.9194 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3672 2.2023 0.2569 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3623 -0.4157 -0.2837 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2680 -0.6661 2.2206 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5044 -1.9724 1.2100 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4864 -0.7715 2.1000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1071 -1.0457 -0.7624 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4569 0.5476 -1.4562 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8379 2.2235 1.8079 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5862 3.4960 0.5253 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4163 2.0781 0.8272 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1068 0.4625 -1.0915 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6926 1.2464 0.3494 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9219 0.0952 0.7436 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3982 0.9909 -2.1523 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7634 2.1105 -0.9224 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5709 2.9915 -1.5831 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2979 1.6870 -0.3297 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3189 3.3604 1.2321 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5403 4.9750 -1.2775 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7189 5.8799 0.3138 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2339 4.8668 -0.0876 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8535 4.5706 0.1859 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8057 2.8974 0.9791 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2422 4.3794 1.9050 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5742 -1.0073 -1.2212 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5477 -2.8179 0.0674 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7689 -4.6370 1.7516 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6797 -2.0616 0.3573 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1092 -3.3624 2.7211 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1867 -2.2475 1.7029 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7931 -3.7903 0.9572 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2863 -6.3456 2.6718 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9159 -1.1232 -2.3517 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5353 -2.0403 -4.3567 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6582 -3.5193 -3.2503 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6757 -3.5883 -4.7430 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 2 0 5 7 1 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 1 0 16 17 1 0 17 18 2 0 17 19 1 0 19 20 1 0 20 21 1 0 20 22 1 0 14 23 1 0 23 24 1 0 24 25 2 0 25 26 1 0 26 27 2 0 27 28 1 0 28 29 2 0 28 30 1 0 30 31 1 0 27 32 1 0 23 33 1 0 33 34 1 0 34 35 1 0 35 36 2 0 35 37 1 0 37 38 1 0 36 11 1 0 34 13 2 0 29 24 1 0 1 39 1 0 1 40 1 0 1 41 1 0 2 42 1 0 3 43 1 0 3 44 1 0 3 45 1 0 4 46 1 0 4 47 1 0 8 48 1 0 8 49 1 0 9 50 1 0 10 51 1 0 12 52 1 0 14 53 1 1 15 54 1 0 15 55 1 0 19 56 1 0 19 57 1 0 20 58 1 0 21 59 1 0 21 60 1 0 21 61 1 0 22 62 1 0 22 63 1 0 22 64 1 0 23 65 1 6 25 66 1 0 26 67 1 0 29 68 1 0 31 69 1 0 31 70 1 0 31 71 1 0 32 72 1 0 36 73 1 0 38 74 1 0 38 75 1 0 38 76 1 0 M END

Standard InCHIKey	HZUKVQHPHZPOEM-PLVUCCGMSA-N
Standard InCHI	InChI=1S/C30H38O8/c1-18(2)12-27(32)36-11-7-8-20-14-22-23(17-37-28(33)13-19(3)4)29(38-30(22)26(15-20)35-6)21-9-10-24(31)25(16-21)34-5/h7-10,14-16,18-19,23,29,31H,11-13,17H2,1-6H3/b8-7+/t23-,29+/m1/s1
SMILES	CC(C)CC(=O)OC/C=C/c1cc2[C@@H](COC(=O)CC(C)C)[C@H](c3ccc(c(c3)OC)O)Oc2c(c1)OC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	526.26	Volume:	548.36 ? Van der Waals volume.
Dense:	0.96	LogP:	5.56 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.272 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-6.862 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	14.0	Rigid Bonds:	19.0
TPSA:	100.52 ? Topological Polar Surface Area.	H-Bond Acceptor:	8.0
H-Bond Donor:	1.0	Rings:	3.0
Heavy Atoms:	8.0

MedChem Properties

QED Drug-Likeness Score:	0.346	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.717	Fsp³:	0.467
MCE-18:	68.0 ? 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:	1	PAINS Alert:	0
Colloidal aggregators:	0.993	Fluc inhibitor:	0.67 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.153 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.935 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.225	Promiscuous compounds:	0.081

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.876	MDCK Permeability:	-4.768
Pgp-inhibitor:	0.002	Pgp-substrate:	0.042
PAMPA:	0.032 ? 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%):	0.417	30% Bioavailability (F30%):	0.243
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.598	MRP1:	0.42
Plasma Protein Binding (PPB):	91.794%	Volume Distribution (VD):	-0.107
Fu:	6.863% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.131
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.795	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	1.0	CYP2C19-substrate:	1.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.003
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.968
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.831 ? 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):

6.526

Half-life (T1/2):

0.759

ADMET: Toxicity

hERG Blockers:	0.251	hERG Blockers (10um):	0.603
Human Hepatotoxicity (H-HT):	0.769	Drug-induced Liver Injury (DILI):	0.633
AMES Toxicity:	0.543	Rat Oral Acute Toxicity:	0.277
Maximum Recommended Daily Dose:	0.645	Skin Sensitization:	0.938
Carcinogencity:	0.803	Eye Corrosion:	0.001
Eye Irritation:	0.223	Respiratory Toxicity:	0.207
Drug-induced Neurotoxicity:	0.616	Ototoxicity:	0.685
Hematotoxicity:	0.417	Drug-induced Nephrotoxicity:	0.887
Genotoxicity:	0.458	RPMI-8226 Immunitoxicity:	0.342
A549 Cytotoxicity:	0.265	Hek293 Cytotoxicity:	0.246
BCF:	1.389 ? 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:	4.187 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.823 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.244 ? 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
NPO40282	Petradoria pumila	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29738243]
NPO40049	Brachanthemum gobicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30896183]
NPO40049	Brachanthemum gobicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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
Organism	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
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	>	20000.0	nM	PMID[29738243]
NPT25810	Organism	Trypanosoma congolense	Trypanosoma congolense	IC50	=	13400.0	nM	PMID[30896183]

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 NPC480698 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	10461
0.1-0.2	34294
0.2-0.3	4694
0.3-0.4	327
0.4-0.5	46
0.5-0.6	24
0.6-0.7	5
0.7-0.8	0
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8571	High Similarity	NPC236166
0.8358	Intermediate Similarity	NPC131971
0.8358	Intermediate Similarity	NPC15189
0.7606	Intermediate Similarity	NPC480704
0.7324	Intermediate Similarity	NPC480707
0.6538	Remote Similarity	NPC216916
0.6538	Remote Similarity	NPC45943
0.6375	Remote Similarity	NPC480705
0.6176	Remote Similarity	NPC15621
0.6145	Remote Similarity	NPC115203
0.5926	Remote Similarity	NPC469889
0.5802	Remote Similarity	NPC180768
0.5775	Remote Similarity	NPC187616
0.5775	Remote Similarity	NPC193026
0.5775	Remote Similarity	NPC49603
0.5747	Remote Similarity	NPC125495
0.5584	Remote Similarity	NPC206413
0.5584	Remote Similarity	NPC482649
0.5584	Remote Similarity	NPC149003
0.5584	Remote Similarity	NPC482647
0.5584	Remote Similarity	NPC482648
0.5584	Remote Similarity	NPC482651
0.5584	Remote Similarity	NPC194244
0.5584	Remote Similarity	NPC482650
0.5422	Remote Similarity	NPC480700
0.5385	Remote Similarity	NPC253878
0.5385	Remote Similarity	NPC471414
0.5325	Remote Similarity	NPC284881
0.5325	Remote Similarity	NPC93433
0.5325	Remote Similarity	NPC474444
0.5263	Remote Similarity	NPC156502
0.5263	Remote Similarity	NPC10737
0.5116	Remote Similarity	NPC107145
0.5111	Remote Similarity	NPC302610

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC480698 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	2770
0.1-0.2	6217
0.2-0.3	158
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