NPASS Compound

Natural Product: NPC165482

Natural Product ID	NPC165482
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Lysidiside O
IUPAC Name	(2S,3R,4R,5R,6S)-2-[(2S,3R,4S,5S,6R)-4,5-dihydroxy-2-[3-hydroxy-5-[(Z)-2-(4-hydroxyphenyl)ethenyl]phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy-6-methyloxane-3,4,5-triol
Synonyms	lysidiside O
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL575219
PubChem CID	25155597
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 70 73 0 0 0 0 0 0 0 0999 V2000 1.7513 0.3428 -4.5480 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4672 0.8188 -4.4302 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5637 -0.2711 -4.3198 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3901 -1.0973 -3.2346 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7237 -0.5395 -2.0147 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2620 0.3382 -1.6494 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0556 0.1958 -0.5338 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9720 -0.8372 0.3737 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8147 -0.9057 1.4795 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7193 -1.9501 2.3837 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7555 0.0783 1.6768 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8954 1.1368 0.8091 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0181 1.1579 -0.2905 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8876 2.1482 0.8839 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0928 2.0624 1.3026 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7831 0.9083 1.7857 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6063 -0.3810 1.3598 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2775 -1.4118 1.9810 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1406 -1.2381 3.0279 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3086 0.0773 3.4436 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6610 1.1158 2.8535 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8090 -2.2860 3.6430 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1191 0.0735 -1.9824 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.7624 -0.3359 -3.2869 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9610 0.3131 -4.3893 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5927 0.0865 -5.5865 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1064 -0.0268 -3.3450 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9043 -0.4235 -0.9630 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3442 0.4983 -0.0600 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8498 0.1488 1.1967 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6385 -0.8668 1.7413 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8884 -1.7171 2.7323 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7984 -0.1517 2.4460 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.3070 0.8813 1.4654 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.8394 0.6070 0.0499 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2955 1.6914 -0.7247 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0207 2.1824 1.8731 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7569 -1.0560 2.8376 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8993 -0.4790 -4.0230 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2559 1.3950 -5.3758 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3991 1.5770 -3.6238 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4558 -0.9054 -5.2249 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7776 -1.3826 -1.3043 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2668 -1.6343 0.2848 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8953 -2.9154 2.1377 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3372 -0.0098 2.5844 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1025 1.9808 -0.9909 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5645 3.1849 0.5206 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7405 2.9964 1.3013 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9669 -0.6067 0.4799 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1022 -2.4090 1.6088 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9955 0.2082 4.2739 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8442 2.1142 3.2341 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4500 -2.8227 3.0807 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9652 1.1669 -1.9088 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6713 -1.4367 -3.3884 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9193 1.4018 -4.1838 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3009 -0.7706 -5.9938 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2941 0.6089 -4.0720 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9741 1.5310 -0.3168 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0865 -1.5225 0.9914 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7540 -1.2346 3.7020 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5193 -2.6227 2.9107 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9631 -2.0819 2.2618 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4118 0.3380 3.3848 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4187 0.7909 1.4681 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3761 -0.2815 -0.2990 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0187 1.4197 -1.3402 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8862 2.2437 2.8555 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4423 -1.2090 2.1424 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 9 11 2 0 11 12 1 0 12 13 2 0 12 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 19 22 1 0 5 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 24 27 1 0 23 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 1 0 31 33 1 0 33 34 1 0 34 35 1 0 35 36 1 0 34 37 1 0 33 38 1 0 25 3 1 0 35 29 1 0 13 7 1 0 21 16 1 0 1 39 1 0 2 40 1 0 2 41 1 0 3 42 1 6 5 43 1 1 8 44 1 0 10 45 1 0 11 46 1 0 13 47 1 0 14 48 1 0 15 49 1 0 17 50 1 0 18 51 1 0 20 52 1 0 21 53 1 0 22 54 1 0 23 55 1 6 24 56 1 6 25 57 1 1 26 58 1 0 27 59 1 0 29 60 1 6 31 61 1 6 32 62 1 0 32 63 1 0 32 64 1 0 33 65 1 1 34 66 1 6 35 67 1 6 36 68 1 0 37 69 1 0 38 70 1 0 M END

Standard InCHIKey	MASPJNQRZIRSFR-MTVVTEEYSA-N
Standard InCHI	InChI=1S/C26H32O12/c1-12-19(30)21(32)23(34)25(35-12)38-24-22(33)20(31)18(11-27)37-26(24)36-17-9-14(8-16(29)10-17)3-2-13-4-6-15(28)7-5-13/h2-10,12,18-34H,11H2,1H3/b3-2-/t12-,18+,19-,20+,21+,22-,23+,24+,25-,26+/m0/s1
SMILES	OC[C@H]1O[C@@H](Oc2cc(O)cc(c2)/C=Cc2ccc(cc2)O)[C@@H]([C@H]([C@@H]1O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	536.19	Volume:	511.054 ? Van der Waals volume.
Dense:	1.049	LogP:	0.907 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.511 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.523 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	7.0	Rigid Bonds:	25.0
TPSA:	198.76 ? Topological Polar Surface Area.	H-Bond Acceptor:	12.0
H-Bond Donor:	8.0	Rings:	4.0
Heavy Atoms:	12.0

MedChem Properties

QED Drug-Likeness Score:	0.207	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.5	Fsp³:	0.462
MCE-18:	95.211 ? 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:	0	PAINS Alert:	0
Colloidal aggregators:	0.633	Fluc inhibitor:	0.989 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.183 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.362 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.562	Promiscuous compounds:	0.295

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.3	MDCK Permeability:	-5.129
Pgp-inhibitor:	0.0	Pgp-substrate:	0.074
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):	0.745
20% Bioavailability (F20%):	0.878	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001	MRP1:	0.014
Plasma Protein Binding (PPB):	76.686%	Volume Distribution (VD):	-0.249
Fu:	24.695% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.024
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.033	CYP2D6-substrate:	0.061
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.134
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.775
HLM stability:	0.05 ? 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):

2.033

Half-life (T1/2):

4.804

ADMET: Toxicity

hERG Blockers:	0.066	hERG Blockers (10um):	0.225
Human Hepatotoxicity (H-HT):	0.846	Drug-induced Liver Injury (DILI):	0.249
AMES Toxicity:	0.946	Rat Oral Acute Toxicity:	0.015
Maximum Recommended Daily Dose:	0.02	Skin Sensitization:	1.0
Carcinogencity:	0.037	Eye Corrosion:	0.0
Eye Irritation:	0.349	Respiratory Toxicity:	0.001
Drug-induced Neurotoxicity:	0.046	Ototoxicity:	0.992
Hematotoxicity:	0.027	Drug-induced Nephrotoxicity:	0.949
Genotoxicity:	0.256	RPMI-8226 Immunitoxicity:	0.312
A549 Cytotoxicity:	0.923	Hek293 Cytotoxicity:	0.691
BCF:	0.353 ? 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:	2.716 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.232 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.47 ? 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
NPO33047	lysidice brevicalyx wei	Species	n.a.	Eukaryota	Barks	n.a.	n.a.	PMID[18847246]

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	2

Activity Type	# Activity
Non-molecular	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
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	Activity	=	11.0	%	PMID[18847246]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	Activity	=	10.0	%	PMID[18847246]

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 NPC165482 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	18228
0.1-0.2	26340
0.2-0.3	4468
0.3-0.4	718
0.4-0.5	73
0.5-0.6	21
0.6-0.7	5
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	NPC138350
0.7808	Intermediate Similarity	NPC89686
0.7808	Intermediate Similarity	NPC257095
0.7746	Intermediate Similarity	NPC238243
0.75	Intermediate Similarity	NPC188555
0.6765	Remote Similarity	NPC85799
0.6765	Remote Similarity	NPC303422
0.6447	Remote Similarity	NPC40664
0.6447	Remote Similarity	NPC197723
0.6329	Remote Similarity	NPC273932
0.589	Remote Similarity	NPC242028
0.589	Remote Similarity	NPC203230
0.5833	Remote Similarity	NPC218003
0.5775	Remote Similarity	NPC607702
0.5676	Remote Similarity	NPC294166
0.5676	Remote Similarity	NPC115022
0.5663	Remote Similarity	NPC475246
0.5658	Remote Similarity	NPC212770
0.5632	Remote Similarity	NPC142860
0.5632	Remote Similarity	NPC152538
0.5632	Remote Similarity	NPC246469
0.5632	Remote Similarity	NPC89088
0.55	Remote Similarity	NPC130496
0.5417	Remote Similarity	NPC214910
0.5395	Remote Similarity	NPC8497
0.5256	Remote Similarity	NPC98777
0.5244	Remote Similarity	NPC3293
0.5233	Remote Similarity	NPC285108
0.5165	Remote Similarity	NPC291124
0.5165	Remote Similarity	NPC131157
0.5109	Remote Similarity	NPC65003

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC165482 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5190
0.1-0.2	3849
0.2-0.3	108
0.3-0.4	3
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