NPASS Compound

Natural Product: NPC53917

Natural Product ID	NPC53917
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Sid85149138
IUPAC Name	[(2R)-3-hydroxy-1-(4-methoxy-7-oxofuro[3,2-g]chromen-9-yl)oxy-3-methylbutan-2-yl] acetate
Synonyms	Sec-O-Acetylbyakangelicin
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL452237
PubChem CID	44144309
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000145] Coumarins and derivatives [CHEMONTID:0000358] Furanocoumarins [CHEMONTID:0002569] Linear furanocoumarins [CHEMONTID:0000202] Psoralens [CHEMONTID:0002832] 5-methoxypsoralens

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 47 49 0 0 0 0 0 0 0 0999 V2000 -5.2938 2.4330 1.7548 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3391 1.3041 1.6351 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2292 0.3939 2.4986 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4804 1.1781 0.5274 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5741 0.0977 0.4236 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1812 0.6818 0.4654 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2705 -0.3875 0.3625 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0918 -0.2576 0.3638 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7774 -0.3017 1.5757 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1668 -0.1670 1.5529 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5664 -0.2465 2.8546 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4040 -0.4240 3.5918 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3709 -0.4522 2.8123 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8280 0.0043 0.3549 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1419 0.0469 -0.8412 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7825 0.2156 -2.0317 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0179 0.2476 -3.1934 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6384 0.1108 -3.1367 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9889 0.1455 -4.2071 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0707 -0.0496 -1.9604 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7489 -0.0864 -0.8372 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1913 0.1350 0.3481 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0112 -1.0130 0.2347 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8105 -0.7480 -0.7893 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1707 -1.3759 -0.6736 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7601 0.0248 -2.0760 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8644 -1.7716 -0.7828 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7495 2.3458 2.7735 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8287 3.4164 1.6915 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1178 2.3788 1.0173 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6781 -0.5585 1.3126 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0784 1.2533 1.4099 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9835 1.3747 -0.3613 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5878 -0.1791 3.1877 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3775 -0.5242 4.6734 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8408 0.3185 -2.0535 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4721 0.3788 -4.1660 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8013 -0.9504 1.0105 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4528 -1.0178 -0.7979 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4323 -1.9472 0.3600 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9197 -0.5654 -0.8225 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2673 -2.1799 -1.4259 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2520 -1.8180 0.3429 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2917 -0.6484 -2.8423 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1862 0.9471 -2.0288 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8041 0.2975 -2.3895 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6305 -2.0600 -1.7188 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 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 1 0 11 12 2 0 12 13 1 0 10 14 2 0 14 15 1 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 18 20 1 0 20 21 1 0 14 22 1 0 22 23 1 0 5 24 1 0 24 25 1 0 24 26 1 0 24 27 1 0 21 8 1 0 13 9 1 0 21 15 2 0 1 28 1 0 1 29 1 0 1 30 1 0 5 31 1 1 6 32 1 0 6 33 1 0 11 34 1 0 12 35 1 0 16 36 1 0 17 37 1 0 23 38 1 0 23 39 1 0 23 40 1 0 25 41 1 0 25 42 1 0 25 43 1 0 26 44 1 0 26 45 1 0 26 46 1 0 27 47 1 0 M END

Standard InCHIKey	LCMMQFCZXXSQDH-CYBMUJFWSA-N
Standard InCHI	InChI=1S/C19H20O8/c1-10(20)26-13(19(2,3)22)9-25-18-16-12(7-8-24-16)15(23-4)11-5-6-14(21)27-17(11)18/h5-8,13,22H,9H2,1-4H3/t13-/m1/s1
SMILES	CC(=O)O[C@H](COc1c2c(cco2)c(c2ccc(=O)oc12)OC)C(C)(C)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
NPO24758.2	Angelica dahurica	Under-species	n.a.	n.a.	root	n.a.	n.a.	PMID[9157191]
NPO24758.2	Angelica dahurica	Under-species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]

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
Potency	7
Activity	2

Activity Type	# Activity
Individual protein	5
Organism	3
Others	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT152	Individual protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	Potency	n.a.	12995.3	nM	DrugMatrix in vitro pharmacology data
NPT135	Individual protein	Chromobox protein homolog 1	Homo sapiens	Potency	n.a.	100000.0	nM	PMID[17315955]
NPT156	Individual protein	Sphingomyelin phosphodiesterase	Homo sapiens	Potency	n.a.	25118.9	nM	PMID[23964704]
NPT539	Individual protein	Cellular tumor antigen p53	Homo sapiens	Potency	n.a.	11220.2	nM	PMID[24191659]
NPT64	Individual protein	ATPase family AAA domain-containing protein 5	Homo sapiens	Potency	n.a.	18348.9	nM	PMID[17573162]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	8275.3	nM	DrugMatrix in vitro pharmacology data
NPT2	Others	Unspecified	n.a.	Potency	n.a.	35481.3	nM	PMID[18541727]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	93.2	%	PMID[26793989]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	151.0	%	PMID[24507920]

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 NPC53917 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	18505
0.1-0.2	30147
0.2-0.3	1043
0.3-0.4	120
0.4-0.5	29
0.5-0.6	8
0.6-0.7	4
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
0.7302	Intermediate Similarity	NPC224165
0.7302	Intermediate Similarity	NPC144288
0.6769	Remote Similarity	NPC107244
0.6716	Remote Similarity	NPC198876
0.6441	Remote Similarity	NPC234536
0.6364	Remote Similarity	NPC210460
0.5972	Remote Similarity	NPC478570
0.5972	Remote Similarity	NPC478569
0.5921	Remote Similarity	NPC478568
0.5882	Remote Similarity	NPC67450
0.5753	Remote Similarity	NPC478567
0.5735	Remote Similarity	NPC155264
0.5616	Remote Similarity	NPC478566
0.56	Remote Similarity	NPC193881

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC53917 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3930
0.1-0.2	5115
0.2-0.3	102
0.3-0.4	1
0.4-0.5	2
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