NPASS Compound

Natural Product: NPC474143

Natural Product ID	NPC474143
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Sargachromanol I
IUPAC Name	(4R,10E)-4-hydroxy-13-[(2R)-6-hydroxy-2,8-dimethyl-3,4-dihydrochromen-2-yl]-2,6,10-trimethyltrideca-2,10-dien-5-one
Synonyms	Sargachromanol I
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL462918
PubChem CID	11441767
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001534] Quinone and hydroquinone lipids [CHEMONTID:0001546] Vitamin E compounds

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 71 72 0 0 0 0 0 0 0 0999 V2000 0.2985 -0.2509 1.6839 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0006 -0.8368 0.3782 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1783 -1.4818 0.2331 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1503 -1.6134 1.3245 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4162 -0.8825 1.1385 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2852 -1.1935 -0.0159 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.7181 -2.6522 -0.0504 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6912 -0.8198 -1.3105 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6233 0.0002 -2.2022 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1421 1.1509 -1.4238 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6211 0.8296 -0.1535 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5480 -0.4915 0.2106 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1236 1.8595 0.6207 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6435 1.5130 1.9873 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1630 3.1608 0.1840 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6909 3.4707 -1.0646 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1797 2.4458 -1.8620 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7011 4.7813 -1.5742 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8804 -0.7009 -0.7770 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1845 -1.3949 -0.6379 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0784 -1.0066 0.4782 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4041 -1.7782 0.4236 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1106 -1.4983 -0.8550 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3748 -2.3967 -1.6356 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4804 -0.0841 -1.1422 C 0 0 1 0 0 0 0 0 0 0 0 0 6.3957 0.4117 -0.0669 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7470 1.6760 -0.0195 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6549 2.1544 1.0517 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2565 2.6806 -1.0276 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1323 0.0299 -2.3658 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2053 -3.2487 0.5981 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5519 0.3973 2.0587 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1553 0.4763 1.6659 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5262 -1.0087 2.4464 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3570 -1.9240 -0.7284 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6283 -1.2494 2.2650 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3217 -2.7056 1.5844 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0207 -1.0099 2.1011 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1899 0.2353 1.1866 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2372 -2.9584 0.8723 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4769 -2.7249 -0.8767 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8863 -3.3198 -0.3401 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8124 -0.1698 -1.1537 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3388 -1.7240 -1.8873 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4846 -0.6587 -2.4376 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1470 0.2840 -3.1392 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1496 2.1040 2.7738 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6487 0.4366 2.1465 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7160 1.8417 1.9857 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5574 3.9383 0.8046 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7940 2.6548 -2.8642 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8938 5.4043 -1.4283 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3262 -1.0528 -1.7051 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0611 0.4039 -0.9941 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0422 -2.5251 -0.5477 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6927 -1.3104 -1.6381 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3147 0.0634 0.4593 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6335 -1.2339 1.4867 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0404 -1.3857 1.2366 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5588 0.5246 -1.1765 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7731 -0.2728 0.6787 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1339 3.1131 0.7692 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4355 1.3815 1.2513 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0822 2.3033 2.0061 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3366 3.7110 -0.6131 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8048 2.5653 -1.9813 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1995 2.4623 -1.2046 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1234 0.0321 -2.2444 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4222 -3.4868 1.3388 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1650 -3.6633 1.0162 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0574 -3.7822 -0.3746 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 1 0 6 5 1 1 6 7 1 0 6 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 11 13 1 0 13 14 1 0 13 15 2 0 15 16 1 0 16 17 2 0 16 18 1 0 2 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 2 0 23 25 1 0 25 26 1 0 26 27 2 3 27 28 1 0 27 29 1 0 25 30 1 0 22 31 1 0 12 6 1 0 17 10 1 0 1 32 1 0 1 33 1 0 1 34 1 0 3 35 1 0 4 36 1 0 4 37 1 0 5 38 1 0 5 39 1 0 7 40 1 0 7 41 1 0 7 42 1 0 8 43 1 0 8 44 1 0 9 45 1 0 9 46 1 0 14 47 1 0 14 48 1 0 14 49 1 0 15 50 1 0 17 51 1 0 18 52 1 0 19 53 1 0 19 54 1 0 20 55 1 0 20 56 1 0 21 57 1 0 21 58 1 0 22 59 1 0 25 60 1 6 26 61 1 0 28 62 1 0 28 63 1 0 28 64 1 0 29 65 1 0 29 66 1 0 29 67 1 0 30 68 1 0 31 69 1 0 31 70 1 0 31 71 1 0 M END

Standard InCHIKey	SARNJEPZDCTAHR-ZAGCOSOKSA-N
Standard InCHI	InChI=1S/C27H40O4/c1-18(2)15-24(29)25(30)20(4)11-7-9-19(3)10-8-13-27(6)14-12-22-17-23(28)16-21(5)26(22)31-27/h10,15-17,20,24,28-29H,7-9,11-14H2,1-6H3/b19-10+/t20?,24-,27-/m1/s1
SMILES	C/C(=CCC[C@]1(C)CCc2c(O1)c(C)cc(c2)O)/CCCC(C(=O)[C@@H](C=C(C)C)O)C

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
NPO11479	Sargassum siliquastrum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15921416]
NPO11479	Sargassum siliquastrum	Species	Sargassaceae	Eukaryota	n.a.	subtidal zone (0-2 m) off the southwestern shore of Jeju Island, Korea	2003-Apr	PMID[18817444]
NPO11479	Sargassum siliquastrum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19006667]
NPO11479	Sargassum siliquastrum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21377877]
NPO11479	Sargassum siliquastrum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28720331]
NPO11479	Sargassum siliquastrum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11479	Sargassum siliquastrum	Species	Sargassaceae	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	2
Activity	1
MIC	6

Activity Type	# Activity
Individual protein	1
Others	2
Organism	6

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1087	Individual protein	Isocitrate lyase	Candida albicans	IC50	>	200.0	ug.mL-1	PMID[16413779]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT729	Organism	Micrococcus luteus	Micrococcus luteus	MIC	>	100.0	ug.mL-1	PMID[1479376]
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	MIC	>	100.0	ug.mL-1	PMID[24611928]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	>	100.0	ug.mL-1	PMID[18077363]
NPT1	Others	Radical scavenging activity	n.a.	Activity	=	90.4	%	PMID[20143840]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	100.0	ug.mL-1	PubChem BioAssay data set
NPT766	Organism	Proteus vulgaris	Proteus vulgaris	MIC	>	100.0	ug.mL-1	PubChem BioAssay data set
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	100.0	ug.mL-1	PMID[9392875]
NPT2	Others	Unspecified	n.a.	IC50	=	60600.0	nM	PMID[19013063]

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 NPC474143 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	7692
0.1-0.2	39305
0.2-0.3	2713
0.3-0.4	91
0.4-0.5	20
0.5-0.6	15
0.6-0.7	19
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
0.8406	Intermediate Similarity	NPC474246
0.7465	Intermediate Similarity	NPC271832
0.7027	Intermediate Similarity	NPC603704
0.6866	Remote Similarity	NPC69539
0.6757	Remote Similarity	NPC59654
0.6712	Remote Similarity	NPC276962
0.6712	Remote Similarity	NPC190086
0.6667	Remote Similarity	NPC610467
0.6622	Remote Similarity	NPC204535
0.6622	Remote Similarity	NPC46586
0.6622	Remote Similarity	NPC609807
0.6486	Remote Similarity	NPC232295
0.6486	Remote Similarity	NPC611336
0.6479	Remote Similarity	NPC32152
0.6479	Remote Similarity	NPC147896
0.64	Remote Similarity	NPC474131
0.6316	Remote Similarity	NPC600119
0.6316	Remote Similarity	NPC601388
0.6282	Remote Similarity	NPC475880
0.6282	Remote Similarity	NPC474130
0.625	Remote Similarity	NPC606596
0.6234	Remote Similarity	NPC196621
0.5949	Remote Similarity	NPC610755
0.5769	Remote Similarity	NPC185634
0.575	Remote Similarity	NPC474237
0.5647	Remote Similarity	NPC475028
0.5647	Remote Similarity	NPC476025
0.561	Remote Similarity	NPC609153
0.5385	Remote Similarity	NPC483459
0.5385	Remote Similarity	NPC483457
0.5385	Remote Similarity	NPC483456
0.5385	Remote Similarity	NPC483458
0.5278	Remote Similarity	NPC187993
0.5278	Remote Similarity	NPC238176
0.52	Remote Similarity	NPC45663
0.5122	Remote Similarity	NPC609806
0.5062	Remote Similarity	NPC483461

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC474143 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3721
0.1-0.2	5363
0.2-0.3	64
0.3-0.4	1
0.4-0.5	0
0.5-0.6	1
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
0.527	Remote Similarity	NPD6671	Approved

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