NPASS Compound

Natural Product: NPC177742

Natural Product ID	NPC177742
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Scorzodihydrostilbene C
IUPAC Name	1-[3-hydroxy-2-[2-(4-hydroxyphenyl)ethyl]-6-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenyl]ethanone
Synonyms	Scorzodihydrostilbene C
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL556267
PubChem CID	42638804
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000253] Stilbenes [CHEMONTID:0000142] Stilbene 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 57 59 0 0 0 0 0 0 0 0999 V2000 1.0093 0.1572 1.6858 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4662 -1.0033 1.0182 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3055 -1.7640 1.7073 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6595 -1.4689 -0.3557 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7007 -2.3071 -0.6357 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7486 -2.6533 0.2948 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0648 -1.9997 0.1999 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0623 -0.5524 0.3704 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3556 -0.0522 1.6307 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4018 1.3001 1.8900 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1519 2.2037 0.8746 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8580 1.6937 -0.3855 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8101 0.3441 -0.6511 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1869 3.5610 1.0788 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8070 -2.8036 -1.9250 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9115 -2.4801 -2.9118 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1068 -1.6508 -2.6139 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2897 -1.1046 -1.3310 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3525 -0.2950 -1.1495 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0045 0.4309 -0.2334 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4060 1.7881 -0.8106 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.8478 1.7795 -1.2519 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.8039 1.3889 -0.1395 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0253 0.5437 0.8490 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.9224 -0.2498 1.7619 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6886 0.6542 2.4947 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2113 -0.2835 0.0794 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2616 2.5214 0.4802 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9630 0.8321 -2.2921 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1401 2.8382 0.0583 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8527 -3.6740 -2.2910 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5860 0.8614 1.1013 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2396 0.7874 2.2307 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6880 -0.2263 2.5140 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8993 -3.7753 0.2124 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2925 -2.5082 1.3380 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6331 -2.3156 -0.7253 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7427 -2.4273 1.0184 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5685 -0.7327 2.4663 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6391 1.6423 2.8963 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6553 2.3820 -1.1915 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5850 -0.0594 -1.6254 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6829 4.2470 0.5479 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0329 -2.8978 -3.9358 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8446 -1.3695 -3.3684 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5576 0.6064 0.7624 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7930 1.9496 -1.7219 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0926 2.7585 -1.6887 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6422 0.7725 -0.5795 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3997 1.2059 1.4743 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3093 -0.8280 2.4523 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6415 -0.8828 1.1986 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1169 1.0025 3.2327 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2490 2.6151 0.5037 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5238 0.0598 -2.0189 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2372 2.7722 0.4293 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4448 -3.3341 -3.0326 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 2 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 11 14 1 0 5 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 24 27 1 0 23 28 1 0 22 29 1 0 21 30 1 0 15 31 1 0 18 4 1 0 27 20 1 0 13 8 1 0 1 32 1 0 1 33 1 0 1 34 1 0 6 35 1 0 6 36 1 0 7 37 1 0 7 38 1 0 9 39 1 0 10 40 1 0 12 41 1 0 13 42 1 0 14 43 1 0 16 44 1 0 17 45 1 0 20 46 1 1 21 47 1 6 22 48 1 6 23 49 1 6 24 50 1 1 25 51 1 0 25 52 1 0 26 53 1 0 28 54 1 0 29 55 1 0 30 56 1 0 31 57 1 0 M END

Standard InCHIKey	IBJOXGCAQZPNTD-MIUGBVLSSA-N
Standard InCHI	InChI=1S/C22H26O9/c1-11(24)18-14(7-4-12-2-5-13(25)6-3-12)15(26)8-9-16(18)30-22-21(29)20(28)19(27)17(10-23)31-22/h2-3,5-6,8-9,17,19-23,25-29H,4,7,10H2,1H3/t17-,19-,20+,21-,22-/m1/s1
SMILES	CC(=O)c1c(CCc2ccc(cc2)O)c(ccc1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	434.16	Volume:	424.056 ? Van der Waals volume.
Dense:	1.024	LogP:	0.496 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.178 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.398 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	7.0	Rigid Bonds:	19.0
TPSA:	156.91 ? Topological Polar Surface Area.	H-Bond Acceptor:	9.0
H-Bond Donor:	6.0	Rings:	3.0
Heavy Atoms:	9.0

MedChem Properties

QED Drug-Likeness Score:	0.337	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.805	Fsp³:	0.409
MCE-18:	69.774 ? 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:	0.44	Fluc inhibitor:	0.076 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.404 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.178 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.104	Promiscuous compounds:	0.089

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.777	MDCK Permeability:	-5.036
Pgp-inhibitor:	0.0	Pgp-substrate:	0.031
PAMPA:	0.999 ? 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):	0.356
20% Bioavailability (F20%):	0.809	30% Bioavailability (F30%):	0.995
50% Bioavailability (F50%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001	MRP1:	0.477
Plasma Protein Binding (PPB):	82.819%	Volume Distribution (VD):	-0.012
Fu:	17.366% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	0.999	BCRP inhibitor:	0.0
BSEP inhibitor:	0.009

ADMET: Metabolism

CYP1A2-inhibitor:	0.071	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.031	CYP2C19-substrate:	0.003
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.003	CYP2D6-substrate:	0.181
CYP3A4-inhibitor:	0.001	CYP3A4-substrate:	0.007
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.998
HLM stability:	0.065 ? 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):

3.885

Half-life (T1/2):

3.173

ADMET: Toxicity

hERG Blockers:	0.113	hERG Blockers (10um):	0.349
Human Hepatotoxicity (H-HT):	0.746	Drug-induced Liver Injury (DILI):	0.523
AMES Toxicity:	0.888	Rat Oral Acute Toxicity:	0.015
Maximum Recommended Daily Dose:	0.052	Skin Sensitization:	0.997
Carcinogencity:	0.184	Eye Corrosion:	0.0
Eye Irritation:	0.178	Respiratory Toxicity:	0.029
Drug-induced Neurotoxicity:	0.017	Ototoxicity:	0.938
Hematotoxicity:	0.288	Drug-induced Nephrotoxicity:	0.681
Genotoxicity:	0.519	RPMI-8226 Immunitoxicity:	0.099
A549 Cytotoxicity:	0.541	Hek293 Cytotoxicity:	0.628
BCF:	0.707 ? 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:	3.368 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.921 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.133 ? 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
NPO10471	Scorzonera radiata	Species	Asteraceae	Eukaryota	n.a.	Mongolian	n.a.	PMID[19271716]
NPO10471	Scorzonera radiata	Species	Asteraceae	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
IC50	1

Activity Type	# Activity
Others	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
NPT1	Others	Radical scavenging activity	n.a.	IC50	=	486380.0	nM	DrugMatrix in vivo data: Biochemistry

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 NPC177742 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	15511
0.1-0.2	28200
0.2-0.3	5128
0.3-0.4	757
0.4-0.5	219
0.5-0.6	36
0.6-0.7	2
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.803	Intermediate Similarity	NPC147596
0.7761	Intermediate Similarity	NPC56735
0.7183	Intermediate Similarity	NPC476203
0.6164	Remote Similarity	NPC61594
0.6029	Remote Similarity	NPC475628
0.5942	Remote Similarity	NPC611586
0.5811	Remote Similarity	NPC259182
0.5775	Remote Similarity	NPC121001
0.5753	Remote Similarity	NPC601828
0.5658	Remote Similarity	NPC106625
0.5652	Remote Similarity	NPC97326
0.5541	Remote Similarity	NPC148273
0.5507	Remote Similarity	NPC106025
0.5493	Remote Similarity	NPC134260
0.5479	Remote Similarity	NPC210192
0.5455	Remote Similarity	NPC40377
0.541	Remote Similarity	NPC142319
0.5405	Remote Similarity	NPC99233
0.5385	Remote Similarity	NPC607365
0.5352	Remote Similarity	NPC477240
0.5309	Remote Similarity	NPC259834
0.5294	Remote Similarity	NPC205054
0.5294	Remote Similarity	NPC23084
0.5278	Remote Similarity	NPC469661
0.5256	Remote Similarity	NPC257963
0.5238	Remote Similarity	NPC294470
0.5217	Remote Similarity	NPC214910
0.5217	Remote Similarity	NPC210015
0.5195	Remote Similarity	NPC308265
0.5195	Remote Similarity	NPC88484
0.5185	Remote Similarity	NPC23817
0.5147	Remote Similarity	NPC218685
0.5139	Remote Similarity	NPC199335
0.5125	Remote Similarity	NPC287294
0.5077	Remote Similarity	NPC60589
0.5077	Remote Similarity	NPC469708
0.5075	Remote Similarity	NPC214454
0.5072	Remote Similarity	NPC19470
0.5068	Remote Similarity	NPC190217
0.5065	Remote Similarity	NPC169248
0.5065	Remote Similarity	NPC72649

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC177742 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3777
0.1-0.2	5200
0.2-0.3	161
0.3-0.4	9
0.4-0.5	3
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