NPASS Compound

Natural Product: NPC486908

Natural Product ID	NPC486908
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	FSSDTZNYEUODHR-NRFANRHFSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001334] Fatty alcohols [CHEMONTID:0002951] Long-chain fatty alcohols

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 66 66 0 0 0 0 0 0 0 0999 V2000 9.5862 0.0153 1.1606 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4168 -0.7839 0.6258 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1570 -0.0820 1.0781 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9135 -0.7689 0.6165 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8251 -0.8578 -0.8918 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5704 -1.5529 -1.3481 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3191 -0.8162 -0.8643 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3152 0.5700 -1.4080 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1162 1.3505 -0.9527 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8687 0.6929 -1.4104 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3855 1.4393 -1.0063 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5046 1.5690 0.4915 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7319 2.3007 0.9178 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0100 1.6714 0.4884 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1927 0.2697 1.0255 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5000 -0.3368 0.5692 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6909 0.4559 1.0196 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9069 -0.2347 0.5137 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4675 0.0471 -0.7159 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5961 -0.5911 -1.1900 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.1931 -1.5539 -0.4029 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6680 -1.8707 0.8367 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5522 -1.2148 1.2639 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.2735 -2.8445 1.6306 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.1363 -0.2746 -2.4496 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5412 -1.4520 -2.7504 O 0 0 0 0 0 0 0 0 0 0 0 0 9.2672 0.9693 1.6352 H 0 0 0 0 0 0 0 0 0 0 0 0 10.0788 -0.6220 1.9271 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3072 0.2349 0.3525 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3871 -1.8163 1.0269 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4523 -0.7497 -0.4634 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1656 0.9479 0.6651 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1164 0.0087 2.1736 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0539 -0.1611 0.9945 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8515 -1.7642 1.0750 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9099 0.1028 -1.3946 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6990 -1.4693 -1.2460 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5203 -2.6006 -1.0377 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2759 -0.7848 0.2310 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4502 -1.4118 -1.2162 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2114 1.1553 -1.1106 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2791 0.5799 -2.5391 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1928 2.3524 -1.4309 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1888 1.4170 0.1548 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9115 0.5346 -2.5027 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8307 -0.3386 -0.9512 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2984 2.4618 -1.4173 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2445 0.8702 -1.3734 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3747 2.0811 0.9384 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5340 0.5571 0.9676 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7193 2.4500 2.0034 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6903 3.3189 0.4578 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1558 1.6841 -0.6087 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8452 2.2779 0.9114 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0955 0.2861 2.1263 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3932 -0.4184 0.6453 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4613 -0.4309 -0.5283 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5686 -1.3363 1.0699 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6736 0.5450 2.1142 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7065 1.4819 0.6057 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0011 0.8034 -1.3378 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.0878 -2.0819 -0.7422 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1564 -1.4844 2.2493 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.2128 -3.1780 1.3911 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.6344 0.6086 -2.4911 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1338 -2.2281 -3.1764 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 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 22 24 1 0 20 25 1 0 6 26 1 0 23 18 1 0 1 27 1 0 1 28 1 0 1 29 1 0 2 30 1 0 2 31 1 0 3 32 1 0 3 33 1 0 4 34 1 0 4 35 1 0 5 36 1 0 5 37 1 0 6 38 1 6 7 39 1 0 7 40 1 0 8 41 1 0 8 42 1 0 9 43 1 0 9 44 1 0 10 45 1 0 10 46 1 0 11 47 1 0 11 48 1 0 12 49 1 0 12 50 1 0 13 51 1 0 13 52 1 0 14 53 1 0 14 54 1 0 15 55 1 0 15 56 1 0 16 57 1 0 16 58 1 0 17 59 1 0 17 60 1 0 19 61 1 0 21 62 1 0 23 63 1 0 24 64 1 0 25 65 1 0 26 66 1 0 M END

Standard InCHIKey	FSSDTZNYEUODHR-NRFANRHFSA-N
Standard InCHI	InChI=1S/C23H40O3/c1-2-3-11-15-21(24)16-13-10-8-6-4-5-7-9-12-14-20-17-22(25)19-23(26)18-20/h17-19,21,24-26H,2-16H2,1H3/t21-/m0/s1
SMILES	CCCCC[C@@H](CCCCCCCCCCCc1cc(cc(c1)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
NPO40590	Penicillium crustosum + Xylaria sp.	Species Co-culture	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[31265288]

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	12
MIC	3

Activity Type	# Activity
Cell line	11
Organism	3
Others	1

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
NPT116	Cell line	HL-60	Homo sapiens	IC50	>	30000.0	nM	PMID[31265288]
NPT111	Cell line	K562	Homo sapiens	IC50	>	30000.0	nM	PMID[31265288]
NPT181	Cell line	Bel-7402	Homo sapiens	IC50	>	30000.0	nM	PMID[31265288]
NPT393	Cell line	HCT-116	Homo sapiens	IC50	>	30000.0	nM	PMID[31265288]
NPT81	Cell line	A549	Homo sapiens	IC50	>	30000.0	nM	PMID[31265288]
NPT165	Cell line	HeLa	Homo sapiens	IC50	>	30000.0	nM	PMID[31265288]
NPT3140	Cell line	MGC-803	Homo sapiens	IC50	>	30000.0	nM	PMID[31265288]
NPT519	Cell line	SH-SY5Y	Homo sapiens	IC50	>	30000.0	nM	PMID[31265288]
NPT306	Cell line	PC-3	Homo sapiens	IC50	>	30000.0	nM	PMID[31265288]
NPT82	Cell line	MDA-MB-231	Homo sapiens	IC50	>	30000.0	nM	PMID[31265288]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	>	200000.0	nM	PMID[31265288]
NPT565	Organism	Vibrio parahaemolyticus	Vibrio parahaemolyticus	MIC	>	200000.0	nM	PMID[31265288]
NPT21742	Cell line	L02	Homo sapiens	IC50	>	30000.0	nM	PMID[31265288]
NPT1177	Organism	Mycobacterium phlei	Mycobacterium phlei	MIC	=	25000.0	nM	PMID[31265288]
NPT2	Others	Unspecified	n.a.	IC50	>	30000.0	nM	PMID[31265288]

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 NPC486908 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	22343
0.1-0.2	25357
0.2-0.3	1870
0.3-0.4	179
0.4-0.5	58
0.5-0.6	22
0.6-0.7	19
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
0.7941	Intermediate Similarity	NPC294186
0.7941	Intermediate Similarity	NPC147310
0.7941	Intermediate Similarity	NPC137415
0.7941	Intermediate Similarity	NPC166313
0.7941	Intermediate Similarity	NPC192032
0.7941	Intermediate Similarity	NPC24407
0.7941	Intermediate Similarity	NPC11280
0.75	Intermediate Similarity	NPC305603
0.7059	Intermediate Similarity	NPC246056
0.675	Remote Similarity	NPC146798
0.675	Remote Similarity	NPC222522
0.675	Remote Similarity	NPC106396
0.675	Remote Similarity	NPC94351
0.675	Remote Similarity	NPC168303
0.65	Remote Similarity	NPC53051
0.65	Remote Similarity	NPC24404
0.65	Remote Similarity	NPC313030
0.6279	Remote Similarity	NPC71002
0.6279	Remote Similarity	NPC249828
0.6042	Remote Similarity	NPC61033
0.6	Remote Similarity	NPC470700
0.6	Remote Similarity	NPC54844
0.6	Remote Similarity	NPC39097
0.6	Remote Similarity	NPC302681
0.6	Remote Similarity	NPC241891
0.6	Remote Similarity	NPC118286
0.6	Remote Similarity	NPC134829
0.6	Remote Similarity	NPC109691
0.5909	Remote Similarity	NPC302219
0.5897	Remote Similarity	NPC59506
0.5833	Remote Similarity	NPC486909
0.5714	Remote Similarity	NPC39664
0.5686	Remote Similarity	NPC486906
0.561	Remote Similarity	NPC3358
0.561	Remote Similarity	NPC306884
0.561	Remote Similarity	NPC603092
0.5556	Remote Similarity	NPC242342
0.5556	Remote Similarity	NPC85479
0.55	Remote Similarity	NPC37802
0.5366	Remote Similarity	NPC488411
0.5366	Remote Similarity	NPC488410
0.5366	Remote Similarity	NPC488409
0.5333	Remote Similarity	NPC166761
0.525	Remote Similarity	NPC123273
0.525	Remote Similarity	NPC318325
0.5217	Remote Similarity	NPC10588
0.5217	Remote Similarity	NPC284011
0.5122	Remote Similarity	NPC244513
0.5106	Remote Similarity	NPC114064
0.5106	Remote Similarity	NPC72947

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC486908 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5901
0.1-0.2	3121
0.2-0.3	116
0.3-0.4	9
0.4-0.5	3
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