NPASS Compound

Natural Product: NPC178054

Natural Product ID	NPC178054
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(2R,3R,4S)-2-(3,4-Dihydroxyphenyl)-4-(2,4,6-Trihydroxyphenyl)Chroman-3,5,7-Triol
IUPAC Name	(2R,3R,4S)-2-(3,4-dihydroxyphenyl)-4-(2,4,6-trihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1223837
PubChem CID	14009028
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0000337] Flavans [CHEMONTID:0003012] Flavan-3-ols [CHEMONTID:0001584] Catechins

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 48 51 0 0 0 0 0 0 0 0999 V2000 2.5004 -1.5191 0.3760 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5879 -2.1997 -0.0990 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7948 -1.5640 -0.3713 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8614 -0.2021 -0.1435 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7856 0.4986 0.3316 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5724 -0.1646 0.6012 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5055 0.6919 1.1111 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1775 0.0741 1.3339 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5569 0.0171 -0.0092 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6810 -0.8990 0.0096 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6298 -0.8910 1.0158 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6984 -1.7877 0.9985 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8369 -2.6930 -0.0062 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9064 -2.7182 -1.0148 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8430 -1.8261 -0.9978 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9460 -1.9156 -2.0532 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9103 -3.5913 -0.0206 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5799 -0.0110 2.0804 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8582 1.4253 -0.3366 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0814 1.8544 -0.8007 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2545 3.1974 -1.0685 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2521 4.1242 -0.8902 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0289 3.6965 -0.4269 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1582 2.3380 -0.1519 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3784 1.8734 0.3154 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4136 5.4776 -1.1560 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0786 0.9241 -0.9775 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1306 -1.0799 2.0499 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0540 0.4965 -0.4003 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8956 -2.2441 -0.8501 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5940 -2.0289 0.5704 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4861 -3.2560 -0.2594 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8918 1.5618 0.4921 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8804 1.0902 2.1043 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4210 0.8316 1.9339 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1986 -0.3212 -0.7647 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4318 -1.7700 1.7908 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0473 -3.4478 -1.7944 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2883 -2.6824 -2.1074 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8118 -3.1770 0.2327 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2150 0.7500 2.2357 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2138 3.5218 -1.4303 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7985 4.3871 -0.2684 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1971 6.0156 -0.7997 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0311 1.2495 -1.0608 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8997 -1.1040 2.6697 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8882 0.1061 0.0254 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1735 -3.1091 -0.4016 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 1 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 13 17 1 0 11 18 1 0 9 19 1 0 19 20 2 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 24 25 1 0 22 26 1 0 20 27 1 0 8 28 1 0 4 29 1 0 3 30 1 0 6 1 1 0 25 7 1 0 15 10 1 0 24 19 1 0 1 31 1 0 2 32 1 0 5 33 1 0 7 34 1 1 8 35 1 1 9 36 1 6 12 37 1 0 14 38 1 0 16 39 1 0 17 40 1 0 18 41 1 0 21 42 1 0 23 43 1 0 26 44 1 0 27 45 1 0 28 46 1 0 29 47 1 0 30 48 1 0 M END

Standard InCHIKey	OKJJBTUOKCQSPH-PWRODBHTSA-N
Standard InCHI	InChI=1S/C21H18O9/c22-9-4-13(26)17(14(27)5-9)19-18-15(28)6-10(23)7-16(18)30-21(20(19)29)8-1-2-11(24)12(25)3-8/h1-7,19-29H/t19-,20+,21+/m0/s1
SMILES	c1cc(c(cc1[C@@H]1[C@@H]([C@@H](c2c(cc(cc2O)O)O)c2c(cc(cc2O1)O)O)O)O)O

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO23907	Grazielia serrata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8413	Echinus auritus	Species	Echinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11409	Trichothecium sympodiale	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13209	Strychnos tomentosa	Species	Loganiaceae	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
Ratio	1
Kb	1

Activity Type	# Activity
Individual protein	2

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT907	Individual protein	Ribonuclease pancreatic	Homo sapiens	Ratio	=	0.7038	n.a.	PMID[20692173]
NPT907	Individual protein	Ribonuclease pancreatic	Homo sapiens	Kb	=	6.76	10'4/M	PMID[20692173]

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 NPC178054 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	24930
0.1-0.2	21223
0.2-0.3	3276
0.3-0.4	264
0.4-0.5	82
0.5-0.6	52
0.6-0.7	10
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
0.7458	Intermediate Similarity	NPC294558
0.7458	Intermediate Similarity	NPC18185
0.7458	Intermediate Similarity	NPC263940
0.7288	Intermediate Similarity	NPC58190
0.7288	Intermediate Similarity	NPC108811
0.7288	Intermediate Similarity	NPC170103
0.7288	Intermediate Similarity	NPC236202
0.7288	Intermediate Similarity	NPC262911
0.7288	Intermediate Similarity	NPC202742
0.7167	Intermediate Similarity	NPC246202
0.7167	Intermediate Similarity	NPC224161
0.7167	Intermediate Similarity	NPC46335
0.7167	Intermediate Similarity	NPC279406
0.7167	Intermediate Similarity	NPC486519
0.6875	Remote Similarity	NPC226809
0.6418	Remote Similarity	NPC278548
0.6182	Remote Similarity	NPC261619
0.6182	Remote Similarity	NPC61477
0.6182	Remote Similarity	NPC78770
0.6182	Remote Similarity	NPC219876
0.6182	Remote Similarity	NPC126029
0.6182	Remote Similarity	NPC15658
0.6154	Remote Similarity	NPC313116
0.6154	Remote Similarity	NPC603340
0.597	Remote Similarity	NPC70409
0.597	Remote Similarity	NPC204770
0.597	Remote Similarity	NPC600551
0.597	Remote Similarity	NPC601980
0.597	Remote Similarity	NPC602065
0.597	Remote Similarity	NPC611024
0.5873	Remote Similarity	NPC96576
0.5862	Remote Similarity	NPC36835
0.5862	Remote Similarity	NPC246162
0.5862	Remote Similarity	NPC9743
0.5862	Remote Similarity	NPC260491
0.5862	Remote Similarity	NPC61506
0.5862	Remote Similarity	NPC240476
0.5797	Remote Similarity	NPC600630
0.5797	Remote Similarity	NPC607896
0.5797	Remote Similarity	NPC611369
0.5789	Remote Similarity	NPC78074
0.5658	Remote Similarity	NPC86630
0.56	Remote Similarity	NPC147743
0.56	Remote Similarity	NPC4809
0.56	Remote Similarity	NPC73517
0.5584	Remote Similarity	NPC106601
0.5584	Remote Similarity	NPC151474
0.5584	Remote Similarity	NPC478340
0.5513	Remote Similarity	NPC212614
0.5513	Remote Similarity	NPC205613
0.55	Remote Similarity	NPC159526
0.5484	Remote Similarity	NPC150670
0.5455	Remote Similarity	NPC82917
0.5429	Remote Similarity	NPC211561
0.5357	Remote Similarity	NPC601844
0.5352	Remote Similarity	NPC272552
0.5352	Remote Similarity	NPC226108
0.5352	Remote Similarity	NPC322899
0.5316	Remote Similarity	NPC478337
0.5316	Remote Similarity	NPC478338
0.5278	Remote Similarity	NPC46283
0.5278	Remote Similarity	NPC469944
0.5278	Remote Similarity	NPC302549
0.5224	Remote Similarity	NPC601999
0.5211	Remote Similarity	NPC601997
0.5211	Remote Similarity	NPC609211
0.5211	Remote Similarity	NPC610665
0.5205	Remote Similarity	NPC44192
0.5135	Remote Similarity	NPC20050
0.5072	Remote Similarity	NPC184245
0.5072	Remote Similarity	NPC187801
0.5072	Remote Similarity	NPC610920
0.5068	Remote Similarity	NPC65333
0.5067	Remote Similarity	NPC306267
0.5067	Remote Similarity	NPC478616
0.5067	Remote Similarity	NPC478339

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC178054 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5211
0.1-0.2	3844
0.2-0.3	84
0.3-0.4	9
0.4-0.5	0
0.5-0.6	0
0.6-0.7	2
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
0.6182	Remote Similarity	NPD1612	Clinical (unspecified phase)
0.6182	Remote Similarity	NPD1613	Phase 4

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