NPASS Compound

Natural Product: NPC470458

Natural Product ID	NPC470458
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Dodoviscin E
IUPAC Name	5,7-dihydroxy-2-[4-hydroxy-3-[(E)-4-hydroxy-3-methylbut-2-enyl]-5-(3-methylbut-2-enyl)phenyl]-3-methoxychromen-4-one
Synonyms	dodoviscin E
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2037151
PubChem CID	57409966
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001615] Flavones [CHEMONTID:0003502] 3'-prenylated flavones

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 61 63 0 0 0 0 0 0 0 0999 V2000 -3.7412 6.2945 -0.8575 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5898 4.9486 -1.2009 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0522 4.2589 0.0317 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8835 3.6552 -0.0627 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2820 2.9640 1.0670 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9658 1.5274 0.8253 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3129 1.1027 0.5555 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6475 -0.2403 0.3181 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3896 -1.1197 0.3705 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7015 -0.7100 0.6445 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9842 0.6169 0.8712 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3030 0.9854 1.1406 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8191 -1.6767 0.7082 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4157 -3.0720 0.5099 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9360 -3.7638 -0.4897 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5410 -5.1771 -0.7073 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9377 -3.1256 -1.4206 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0237 -0.5842 0.0039 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8773 0.4302 -0.2276 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1196 0.2891 -0.5176 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8648 1.4496 -0.7274 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1916 1.3847 -1.0394 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9201 2.5445 -1.2448 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7646 0.1282 -1.1389 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0407 -1.0309 -0.9345 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7183 -0.9556 -0.6235 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9060 -2.0338 -0.3990 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3978 -3.1751 -0.4825 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5676 -1.8185 -0.0870 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7969 -2.9413 0.1393 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7902 -3.4688 1.4835 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6371 -2.2828 -1.0401 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8593 4.2997 1.2940 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0494 6.8551 -1.2856 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5540 4.5127 -1.4981 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8482 4.8917 -2.0086 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3669 3.6828 -1.0114 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9650 2.9414 1.9682 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3470 3.4187 1.4566 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0968 1.8344 0.5237 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2681 -2.1479 0.1869 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9709 1.1552 0.3958 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2292 -1.6066 1.7474 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5709 -1.3970 -0.0395 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7005 -3.5729 1.1522 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4707 -5.3356 -1.7940 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5812 -5.3720 -0.1889 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2726 -5.8988 -0.2954 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2475 -3.8584 -2.1719 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8386 -2.8082 -0.8314 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4839 -2.2683 -1.9554 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3786 2.4142 -0.6403 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9779 2.9218 -2.1835 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8103 0.0818 -1.3846 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6280 -4.1934 1.5071 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8592 -4.0060 1.6980 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8844 -2.6550 2.2279 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1857 -2.4295 -1.8953 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5077 5.2177 1.2091 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4946 3.4219 1.3957 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2291 4.4967 2.1931 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 1 0 6 7 2 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 11 12 1 0 10 13 1 0 13 14 1 0 14 15 2 3 15 16 1 0 15 17 1 0 8 18 1 0 18 19 1 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 1 0 22 24 2 0 24 25 1 0 25 26 2 0 26 27 1 0 27 28 2 0 27 29 1 0 29 30 1 0 30 31 1 0 25 32 1 0 3 33 1 0 11 6 1 0 29 18 2 0 26 20 1 0 1 34 1 0 2 35 1 0 2 36 1 0 4 37 1 0 5 38 1 0 5 39 1 0 7 40 1 0 9 41 1 0 12 42 1 0 13 43 1 0 13 44 1 0 14 45 1 0 16 46 1 0 16 47 1 0 16 48 1 0 17 49 1 0 17 50 1 0 17 51 1 0 21 52 1 0 23 53 1 0 24 54 1 0 31 55 1 0 31 56 1 0 31 57 1 0 32 58 1 0 33 59 1 0 33 60 1 0 33 61 1 0 M END

Standard InCHIKey	DYGOJNXBKFEBBQ-GIDUJCDVSA-N
Standard InCHI	InChI=1S/C26H28O7/c1-14(2)5-7-16-9-18(10-17(23(16)30)8-6-15(3)13-27)25-26(32-4)24(31)22-20(29)11-19(28)12-21(22)33-25/h5-6,9-12,27-30H,7-8,13H2,1-4H3/b15-6+
SMILES	OC/C(=C/Cc1cc(cc(c1O)CC=C(C)C)c1oc2cc(O)cc(c2c(=O)c1OC)O)/C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	452.18	Volume:	467.75 ? Van der Waals volume.
Dense:	0.967	LogP:	4.479 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.315 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.672 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	7.0	Rigid Bonds:	20.0
TPSA:	120.36 ? Topological Polar Surface Area.	H-Bond Acceptor:	7.0
H-Bond Donor:	4.0	Rings:	3.0
Heavy Atoms:	7.0

MedChem Properties

QED Drug-Likeness Score:	0.387	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.175	Fsp³:	0.269
MCE-18:	22.0 ? 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:	0	PAINS Alert:	0
Colloidal aggregators:	0.884	Fluc inhibitor:	0.617 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.874 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.705 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.214	Promiscuous compounds:	0.068

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.204	MDCK Permeability:	-4.847
Pgp-inhibitor:	0.941	Pgp-substrate:	0.012
PAMPA:	0.189 ? 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):	0.28
20% Bioavailability (F20%):	0.999	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.097
Plasma Protein Binding (PPB):	95.294%	Volume Distribution (VD):	0.166
Fu:	4.377% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.029
OATP1B3 inhibitor:	0.988	BCRP inhibitor:	1.0
BSEP inhibitor:	0.989

ADMET: Metabolism

CYP1A2-inhibitor:	0.001	CYP1A2-substrate:	0.902
CYP2C19-inhibitor:	0.057	CYP2C19-substrate:	0.994
CYP2C9-inhibitor:	0.368	CYP2C9-substrate:	0.001
CYP2D6-inhibitor:	1.0	CYP2D6-substrate:	0.111
CYP3A4-inhibitor:	0.035	CYP3A4-substrate:	0.961
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.998 ? 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):

5.286

Half-life (T1/2):

1.027

ADMET: Toxicity

hERG Blockers:	0.042	hERG Blockers (10um):	0.507
Human Hepatotoxicity (H-HT):	0.69	Drug-induced Liver Injury (DILI):	0.813
AMES Toxicity:	0.437	Rat Oral Acute Toxicity:	0.709
Maximum Recommended Daily Dose:	0.755	Skin Sensitization:	0.944
Carcinogencity:	0.493	Eye Corrosion:	0.0
Eye Irritation:	0.769	Respiratory Toxicity:	0.961
Drug-induced Neurotoxicity:	0.152	Ototoxicity:	0.325
Hematotoxicity:	0.147	Drug-induced Nephrotoxicity:	0.21
Genotoxicity:	0.998	RPMI-8226 Immunitoxicity:	0.099
A549 Cytotoxicity:	0.409	Hek293 Cytotoxicity:	0.776
BCF:	1.842 ? 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:	4.767 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.189 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.634 ? 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
NPO12477	Dodonaea viscosa	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19719093]
NPO12477	Dodonaea viscosa	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22512738]
NPO12477	Dodonaea viscosa	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12477	Dodonaea viscosa	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12477	Dodonaea viscosa	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12477	Dodonaea viscosa	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12477	Dodonaea viscosa	Species	Sapindaceae	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
Activity	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
NPT520	Cell line	3T3-L1	Mus musculus	Activity	=	280.2	%	PMID[24533857]

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 NPC470458 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	21221
0.1-0.2	24581
0.2-0.3	3039
0.3-0.4	772
0.4-0.5	215
0.5-0.6	13
0.6-0.7	11
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8983	High Similarity	NPC158874
0.7971	Intermediate Similarity	NPC470460
0.7879	Intermediate Similarity	NPC470459
0.7846	Intermediate Similarity	NPC97255
0.7612	Intermediate Similarity	NPC269285
0.697	Remote Similarity	NPC246478
0.6438	Remote Similarity	NPC158761
0.6351	Remote Similarity	NPC470457
0.6338	Remote Similarity	NPC259632
0.6316	Remote Similarity	NPC470462
0.625	Remote Similarity	NPC56786
0.6184	Remote Similarity	NPC470461
0.6154	Remote Similarity	NPC59951
0.6	Remote Similarity	NPC123886
0.6	Remote Similarity	NPC184536
0.6	Remote Similarity	NPC103342
0.5909	Remote Similarity	NPC286342
0.5909	Remote Similarity	NPC610359
0.5882	Remote Similarity	NPC162351
0.5882	Remote Similarity	NPC603596
0.5797	Remote Similarity	NPC279989
0.5735	Remote Similarity	NPC82325
0.5694	Remote Similarity	NPC205046
0.56	Remote Similarity	NPC224714
0.5405	Remote Similarity	NPC301217
0.5405	Remote Similarity	NPC200694
0.5405	Remote Similarity	NPC306488
0.5366	Remote Similarity	NPC80534
0.506	Remote Similarity	NPC470456

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC470458 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3983
0.1-0.2	5104
0.2-0.3	56
0.3-0.4	6
0.4-0.5	1
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