NPASS Compound

Natural Product: NPC470457

Natural Product ID	NPC470457
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Dodoviscin B
IUPAC Name	5,7-dihydroxy-2-[4-hydroxy-3-(2-hydroxy-3-methylbut-3-enyl)-5-(3-methylbut-2-enyl)phenyl]-3,6-dimethoxychromen-4-one
Synonyms	dodoviscin B
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2037149
PubChem CID	57409963
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 65 67 0 0 0 0 0 0 0 0999 V2000 -1.2680 4.9672 -0.2254 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4820 4.2797 -0.7122 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9447 3.2253 -0.0832 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2559 2.7174 1.1161 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8285 1.3224 0.9155 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7260 0.2654 1.0018 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3356 -1.0354 0.8127 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9865 -1.2699 0.5259 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0601 -0.2791 0.4295 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5181 1.0430 0.6331 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3633 -0.4590 0.1793 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9923 -1.6589 0.2486 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3772 -1.6820 -0.0214 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9477 -2.7766 0.0402 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0744 -0.5403 -0.3411 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3508 0.6324 -0.3851 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0787 0.6478 -0.1372 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0117 1.8178 -0.7038 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3719 1.8292 -0.9737 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0987 0.6337 -0.9269 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4221 -0.5194 -0.6102 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1193 -1.7104 -0.5581 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4473 0.6369 -1.1934 O 0 0 0 0 0 0 0 0 0 0 0 0 8.4370 0.8265 -0.1940 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0331 3.0130 -1.2925 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3523 -2.8378 0.5735 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3520 -3.2168 1.9673 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2761 -2.1691 0.8979 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1528 -2.3358 -0.3097 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0401 -3.5078 -0.0726 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3589 -3.3818 -0.0641 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4795 -4.8585 0.1617 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4057 -2.6397 -1.4511 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0561 0.5019 1.2863 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1745 4.7879 -1.9195 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4288 4.2654 -0.2109 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0375 5.8765 -0.8237 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4537 5.2768 0.8419 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8473 2.6886 -0.4190 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9703 2.7975 1.9747 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3788 3.3198 1.3823 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7091 -2.2849 0.3507 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1650 1.8781 0.5705 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4900 2.7622 -0.7512 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1975 -2.1510 0.3616 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0284 1.7069 -0.4813 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0842 -0.0771 -0.2087 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9901 0.9358 0.8169 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9654 3.1634 -0.9066 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0436 -2.5776 2.5505 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3446 -3.1125 2.4064 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7514 -4.2623 2.0551 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7184 -3.0814 1.1780 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9843 -1.9984 1.7629 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7099 -1.4174 -0.4843 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7769 -2.3979 -0.2353 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0227 -4.2115 0.1047 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1296 -5.3599 0.9319 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4420 -4.8574 0.5105 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5927 -5.4570 -0.7891 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5546 -3.0964 -1.2003 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7274 0.7157 0.5785 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2540 4.9065 -1.6927 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0774 4.0200 -2.7361 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7257 5.7605 -2.2496 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 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 13 15 1 0 15 16 2 0 16 17 1 0 16 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 20 23 1 0 23 24 1 0 19 25 1 0 12 26 1 0 26 27 1 0 7 28 1 0 28 29 1 0 29 30 1 0 30 31 2 0 30 32 1 0 29 33 1 0 6 34 1 0 2 35 1 0 10 5 1 0 17 11 1 0 21 15 1 0 1 36 1 0 1 37 1 0 1 38 1 0 3 39 1 0 4 40 1 0 4 41 1 0 8 42 1 0 10 43 1 0 18 44 1 0 22 45 1 0 24 46 1 0 24 47 1 0 24 48 1 0 25 49 1 0 27 50 1 0 27 51 1 0 27 52 1 0 28 53 1 0 28 54 1 0 29 55 1 0 31 56 1 0 31 57 1 0 32 58 1 0 32 59 1 0 32 60 1 0 33 61 1 0 34 62 1 0 35 63 1 0 35 64 1 0 35 65 1 0 M END

Standard InCHIKey	FNHZTQPLQXIFKH-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C27H30O8/c1-13(2)7-8-15-9-17(10-16(22(15)30)11-18(28)14(3)4)25-27(34-6)24(32)21-20(35-25)12-19(29)26(33-5)23(21)31/h7,9-10,12,18,28-31H,3,8,11H2,1-2,4-6H3
SMILES	CC(=CCC1=C(C(=CC(=C1)C2=C(C(=O)C3=C(O2)C=C(C(=C3O)OC)O)OC)CC(C(=C)C)O)O)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	482.19	Volume:	493.836 ? Van der Waals volume.
Dense:	0.976	LogP:	4.462 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.219 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.181 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	8.0	Rigid Bonds:	20.0
TPSA:	129.59 ? Topological Polar Surface Area.	H-Bond Acceptor:	8.0
H-Bond Donor:	4.0	Rings:	3.0
Heavy Atoms:	8.0

MedChem Properties

QED Drug-Likeness Score:	0.343	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.706	Fsp³:	0.296
MCE-18:	48.0 ? 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:	0.662	Fluc inhibitor:	0.288 ? 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:	0.677 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.082	Promiscuous compounds:	0.044

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.057	MDCK Permeability:	-4.72
Pgp-inhibitor:	0.117	Pgp-substrate:	0.023
PAMPA:	0.495 ? 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):	0.02
20% Bioavailability (F20%):	0.818	30% Bioavailability (F30%):	0.996
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001	MRP1:	0.812
Plasma Protein Binding (PPB):	95.824%	Volume Distribution (VD):	-0.005
Fu:	3.621% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.103
OATP1B3 inhibitor:	0.994	BCRP inhibitor:	0.999
BSEP inhibitor:	0.804

ADMET: Metabolism

CYP1A2-inhibitor:	0.848	CYP1A2-substrate:	0.999
CYP2C19-inhibitor:	0.664	CYP2C19-substrate:	0.978
CYP2C9-inhibitor:	0.004	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.983	CYP2D6-substrate:	0.329
CYP3A4-inhibitor:	0.098	CYP3A4-substrate:	0.688
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	1.0 ? 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):

5.651

Half-life (T1/2):

1.089

ADMET: Toxicity

hERG Blockers:	0.046	hERG Blockers (10um):	0.482
Human Hepatotoxicity (H-HT):	0.453	Drug-induced Liver Injury (DILI):	0.27
AMES Toxicity:	0.307	Rat Oral Acute Toxicity:	0.483
Maximum Recommended Daily Dose:	0.735	Skin Sensitization:	0.827
Carcinogencity:	0.582	Eye Corrosion:	0.001
Eye Irritation:	0.717	Respiratory Toxicity:	0.774
Drug-induced Neurotoxicity:	0.197	Ototoxicity:	0.713
Hematotoxicity:	0.174	Drug-induced Nephrotoxicity:	0.241
Genotoxicity:	0.728	RPMI-8226 Immunitoxicity:	0.051
A549 Cytotoxicity:	0.201	Hek293 Cytotoxicity:	0.293
BCF:	1.628 ? 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:	4.537 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.008 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.509 ? 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	=	328.1	%	PMID[23398362]

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 NPC470457 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	19863
0.1-0.2	26079
0.2-0.3	3202
0.3-0.4	627
0.4-0.5	68
0.5-0.6	11
0.6-0.7	3
0.7-0.8	0
0.8-0.85	1
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8636	High Similarity	NPC158761
0.8548	High Similarity	NPC246478
0.806	Intermediate Similarity	NPC470459
0.7778	Intermediate Similarity	NPC470456
0.7639	Intermediate Similarity	NPC470462
0.6667	Remote Similarity	NPC158874
0.6351	Remote Similarity	NPC470458
0.6076	Remote Similarity	NPC470460
0.5867	Remote Similarity	NPC97255
0.5821	Remote Similarity	NPC472438
0.5789	Remote Similarity	NPC224714
0.5735	Remote Similarity	NPC266960
0.5714	Remote Similarity	NPC269285
0.5714	Remote Similarity	NPC29841
0.5507	Remote Similarity	NPC203891
0.5493	Remote Similarity	NPC115798
0.5429	Remote Similarity	NPC163524
0.5352	Remote Similarity	NPC9609
0.5195	Remote Similarity	NPC306488

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC470457 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3914
0.1-0.2	5182
0.2-0.3	50
0.3-0.4	3
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