NPASS Compound

Natural Product: NPC50504

Natural Product ID	NPC50504
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	TXLQONQJSWSJJX-CMWLGVBASA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	14583643
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0000507] Isoflavonoid O-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 51 54 0 0 0 0 0 0 0 0999 V2000 4.7311 1.8677 -1.6597 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7347 2.5365 -0.9757 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0067 2.2826 0.3392 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2521 1.3257 1.0034 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2663 0.6761 0.3127 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9658 0.9080 -1.0138 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8977 0.1711 -1.6769 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0785 -0.3614 -2.9359 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1398 -1.0292 -3.5607 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9369 -1.2510 -3.0388 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0152 -1.9660 -3.7510 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2535 -2.1827 -3.1894 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5257 -1.6875 -1.9334 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5804 -0.9805 -1.2324 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6939 -0.7452 -1.7846 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6614 -0.0388 -1.1028 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4096 0.4118 0.0432 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7448 -0.4417 0.0263 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9083 -0.5369 0.7807 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6695 -1.2163 2.1186 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0002 -1.3197 2.8110 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.6039 0.0800 2.9340 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.7173 0.6161 1.5238 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3532 1.9947 1.5043 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6626 2.8839 2.2890 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4183 0.7581 1.0374 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8663 0.0238 3.5083 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9120 -1.8631 4.0766 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1784 -2.4844 1.8952 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2268 -2.9090 -3.9079 O 0 0 0 0 0 0 0 0 0 0 0 0 7.0252 2.9685 1.0148 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5067 2.0585 -2.6959 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3331 3.2892 -1.4865 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4528 1.1039 2.0634 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6848 -0.0649 0.8337 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0407 -0.2145 -3.4169 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2056 -2.3495 -4.7318 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5001 -1.8683 -1.5130 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7003 -1.0948 0.2687 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9706 -0.6516 2.7432 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7038 -1.8864 2.1494 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9396 0.7322 3.5162 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2917 -0.0660 0.8751 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4037 1.8931 1.7718 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2920 2.3349 0.4327 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9799 3.3785 1.7939 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5520 0.0292 2.7938 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1500 -2.8095 4.0598 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6695 -2.5267 1.0377 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9546 -3.5785 -4.6171 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7209 3.8000 1.5345 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 14 18 1 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 23 26 1 0 22 27 1 0 21 28 1 0 20 29 1 0 12 30 1 0 3 31 1 0 6 1 1 0 16 7 1 0 26 19 1 0 15 10 1 0 1 32 1 0 2 33 1 0 4 34 1 0 5 35 1 0 8 36 1 0 11 37 1 0 13 38 1 0 19 39 1 6 20 40 1 1 21 41 1 6 22 42 1 1 23 43 1 6 24 44 1 0 24 45 1 0 25 46 1 0 27 47 1 0 28 48 1 0 29 49 1 0 30 50 1 0 31 51 1 0 M END

Standard InCHIKey	TXLQONQJSWSJJX-CMWLGVBASA-N
Standard InCHI	InChI=1S/C21H20O10/c22-7-15-18(26)19(27)20(28)21(31-15)30-14-6-11(24)5-13-16(14)17(25)12(8-29-13)9-1-3-10(23)4-2-9/h1-6,8,15,18-24,26-28H,7H2/t15-,18-,19+,20-,21-/m1/s1
SMILES	c1cc(ccc1c1coc2cc(cc(c2c1=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	432.11	Volume:	404.357 ? Van der Waals volume.
Dense:	1.069	LogP:	0.612 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.18 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.931 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	24.0
TPSA:	170.05 ? Topological Polar Surface Area.	H-Bond Acceptor:	10.0
H-Bond Donor:	6.0	Rings:	4.0
Heavy Atoms:	10.0

MedChem Properties

QED Drug-Likeness Score:	0.331	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.876	Fsp³:	0.286
MCE-18:	84.259 ? 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:	0.576	Fluc inhibitor:	0.271 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.838 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.671 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.258	Promiscuous compounds:	0.372

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.403	MDCK Permeability:	-5.064
Pgp-inhibitor:	0.0	Pgp-substrate:	0.18
PAMPA:	0.997 ? 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):	0.213
20% Bioavailability (F20%):	0.547	30% Bioavailability (F30%):	0.963
50% Bioavailability (F50%):	0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.02	MRP1:	0.094
Plasma Protein Binding (PPB):	82.537%	Volume Distribution (VD):	-0.116
Fu:	18.001% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.985
OATP1B3 inhibitor:	0.978	BCRP inhibitor:	0.156
BSEP inhibitor:	0.01

ADMET: Metabolism

CYP1A2-inhibitor:	0.831	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.005
CYP2D6-inhibitor:	0.009	CYP2D6-substrate:	0.03
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.071
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.998
HLM stability:	0.0 ? 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):

3.274

Half-life (T1/2):

3.398

ADMET: Toxicity

hERG Blockers:	0.051	hERG Blockers (10um):	0.168
Human Hepatotoxicity (H-HT):	0.693	Drug-induced Liver Injury (DILI):	0.908
AMES Toxicity:	0.864	Rat Oral Acute Toxicity:	0.063
Maximum Recommended Daily Dose:	0.153	Skin Sensitization:	0.988
Carcinogencity:	0.427	Eye Corrosion:	0.0
Eye Irritation:	0.558	Respiratory Toxicity:	0.035
Drug-induced Neurotoxicity:	0.029	Ototoxicity:	0.87
Hematotoxicity:	0.124	Drug-induced Nephrotoxicity:	0.437
Genotoxicity:	0.94	RPMI-8226 Immunitoxicity:	0.062
A549 Cytotoxicity:	0.299	Hek293 Cytotoxicity:	0.571
BCF:	0.407 ? 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:	2.953 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.282 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.519 ? 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
NPO26828	Barbarea verna	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25482	Phyllogeiton zeyheri	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23780	Psoroma crassum	Species	Pannariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26183	Scabiosa pyrenaica	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26828	Barbarea verna	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25482	Phyllogeiton zeyheri	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO2201	Orthocaulis attenuatus	Species	Anastrophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25532	Blitum virgatum	Species	Chenopodiaceae	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

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

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 NPC50504 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	17762
0.1-0.2	27764
0.2-0.3	3090
0.3-0.4	962
0.4-0.5	225
0.5-0.6	31
0.6-0.7	13
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	Natural Product ID
0.76	Intermediate Similarity	NPC100720
0.7273	Intermediate Similarity	NPC479401
0.7105	Intermediate Similarity	NPC197896
0.7105	Intermediate Similarity	NPC313163
0.6883	Remote Similarity	NPC105511
0.6883	Remote Similarity	NPC161749
0.6753	Remote Similarity	NPC83283
0.6709	Remote Similarity	NPC205076
0.6667	Remote Similarity	NPC258035
0.6456	Remote Similarity	NPC156457
0.6386	Remote Similarity	NPC479407
0.6324	Remote Similarity	NPC7013
0.6265	Remote Similarity	NPC479406
0.625	Remote Similarity	NPC609879
0.6125	Remote Similarity	NPC348541
0.6024	Remote Similarity	NPC479402
0.6023	Remote Similarity	NPC479405
0.5976	Remote Similarity	NPC73511
0.5955	Remote Similarity	NPC479404
0.5926	Remote Similarity	NPC259070
0.5926	Remote Similarity	NPC211014
0.5904	Remote Similarity	NPC138540
0.5833	Remote Similarity	NPC481043
0.5833	Remote Similarity	NPC80140
0.5714	Remote Similarity	NPC222936
0.5714	Remote Similarity	NPC599850
0.5632	Remote Similarity	NPC48773
0.561	Remote Similarity	NPC45165
0.561	Remote Similarity	NPC135345
0.5476	Remote Similarity	NPC234739
0.5402	Remote Similarity	NPC229729
0.5341	Remote Similarity	NPC307518
0.5326	Remote Similarity	NPC303913
0.5294	Remote Similarity	NPC603782
0.5287	Remote Similarity	NPC224462
0.5263	Remote Similarity	NPC109187
0.525	Remote Similarity	NPC78697
0.5238	Remote Similarity	NPC160515
0.5176	Remote Similarity	NPC77672
0.5176	Remote Similarity	NPC133671
0.5176	Remote Similarity	NPC135391
0.5176	Remote Similarity	NPC78263
0.5176	Remote Similarity	NPC250069
0.5116	Remote Similarity	NPC323593
0.5116	Remote Similarity	NPC203500
0.5057	Remote Similarity	NPC100818
0.5057	Remote Similarity	NPC610763
0.5056	Remote Similarity	NPC601607

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC50504 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4834
0.1-0.2	4215
0.2-0.3	87
0.3-0.4	9
0.4-0.5	3
0.5-0.6	1
0.6-0.7	1
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
0.6883	Remote Similarity	NPD4381	Clinical (unspecified phase)
0.561	Remote Similarity	NPD3818	Discontinued

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