NPASS Compound

Natural Product: NPC48017

Natural Product ID	NPC48017
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	KVFRGYJDJMIUHN-XYNRRMKTSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL509964
PubChem CID	11657121
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids [CHEMONTID:0002051] Agarofurans

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 2D 80 84 0 0 0 0 0 0 0 0999 V2000 -1.5305 -1.3311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4980 -2.4192 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1000 -3.7949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5903 -3.9648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4827 -2.7591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8943 -1.3846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3943 -1.3846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8943 -1.3846 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6443 -2.6836 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2309 -4.1255 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1443 -2.6836 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8943 -3.9826 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3943 -3.9826 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.1443 -2.6836 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3943 -1.3846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8943 -1.3846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6443 -0.0855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8943 1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3943 1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2760 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3943 -1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0323 -0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0323 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5241 0.5932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3442 2.2172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3907 1.0037 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0788 2.4709 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8068 3.2659 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1935 3.4746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7934 0.8787 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5329 2.3559 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4009 3.3401 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6820 3.3201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0915 2.8070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2406 3.7712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9801 5.2484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5706 5.7615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4215 4.7973 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5151 -3.8472 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9737 -3.4972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0252 -2.4275 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0061 -4.5853 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6879 -0.3769 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6186 -2.3635 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7245 -0.0660 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7489 -3.2470 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3586 -4.1449 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1914 -5.2921 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1642 -5.4030 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9327 -4.6342 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9472 -2.4347 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0986 -0.0602 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3943 -2.8846 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3082 -5.3634 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1443 -5.2817 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 11.6443 -2.6836 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1443 -0.0855 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1443 -0.0855 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0626 -0.5738 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2841 2.5838 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1378 2.0524 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6805 2.6860 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6004 -0.7041 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0159 0.4364 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8615 2.0548 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5503 -0.9066 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6560 3.6844 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8384 2.0865 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0040 2.8749 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0323 4.7182 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1898 4.5893 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4371 2.6359 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3520 1.3298 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6501 3.2582 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1292 6.2126 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3101 7.2387 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0119 5.3103 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8982 -5.7912 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0943 -3.5529 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9180 -5.6178 0.0000 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 1 7 8 1 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 6 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 6 22 23 1 0 23 24 1 0 23 25 1 0 20 26 1 0 26 27 1 0 27 28 2 0 27 29 1 0 17 30 1 0 30 31 1 0 31 32 2 0 31 33 1 0 33 34 2 0 34 35 1 0 35 36 2 0 36 37 1 0 37 38 2 0 5 39 1 0 39 40 1 0 40 41 2 0 40 42 1 0 21 2 1 0 38 33 1 0 21 6 1 0 16 11 1 0 23 19 1 0 1 43 1 0 1 44 1 0 1 45 1 0 2 46 1 6 3 47 1 0 3 48 1 0 4 49 1 0 4 50 1 0 5 51 1 6 7 52 1 0 7 53 1 0 12 54 1 0 13 55 1 0 14 56 1 0 15 57 1 0 16 58 1 0 17 59 1 1 18 60 1 0 18 61 1 0 19 62 1 1 20 63 1 6 24 64 1 0 24 65 1 0 24 66 1 0 25 67 1 0 25 68 1 0 25 69 1 0 29 70 1 0 29 71 1 0 29 72 1 0 34 73 1 0 35 74 1 0 36 75 1 0 37 76 1 0 38 77 1 0 42 78 1 0 42 79 1 0 42 80 1 0 M END

Standard InCHIKey	KVFRGYJDJMIUHN-XYNRRMKTSA-N
Standard InCHI	InChI=1S/C33H38O9/c1-20-16-17-26(39-21(2)34)32(19-38-29(36)23-12-8-6-9-13-23)27(41-30(37)24-14-10-7-11-15-24)18-25-28(40-22(3)35)33(20,32)42-31(25,4)5/h6-15,20,25-28H,16-19H2,1-5H3/t20-,25-,26+,27+,28-,32+,33-/m1/s1
SMILES	C[C@@H]1CC[C@@H]([C@@]2(COC(=O)c3ccccc3)[C@H](C[C@@H]3[C@H]([C@]12OC3(C)C)OC(=O)C)OC(=O)c1ccccc1)OC(=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
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	stem	n.a.	n.a.	PMID[16643054]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	leaves	n.a.	n.a.	PMID[17125218]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	n.a.	root	n.a.	PMID[17315960]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	roots	n.a.	n.a.	PMID[17315960]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18590313]
NPO22423	Microtropis fokienensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22423	Microtropis fokienensis	Species	Celastraceae	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 Type	# Activity
Cell line	2

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
NPT168	Cell line	P388	Mus musculus	IC50	=	43.0	nM	PMID[12542359]
NPT139	Cell line	HT-29	Homo sapiens	IC50	=	71.0	nM	PMID[24900585]

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 NPC48017 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	13219
0.1-0.2	34192
0.2-0.3	1853
0.3-0.4	439
0.4-0.5	82
0.5-0.6	39
0.6-0.7	22
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9333	High Similarity	NPC246480
0.8852	High Similarity	NPC17877
0.7742	Intermediate Similarity	NPC474608
0.7463	Intermediate Similarity	NPC139067
0.7463	Intermediate Similarity	NPC43241
0.7188	Intermediate Similarity	NPC283375
0.7188	Intermediate Similarity	NPC183122
0.6957	Remote Similarity	NPC67777
0.6957	Remote Similarity	NPC177340
0.6901	Remote Similarity	NPC266265
0.6571	Remote Similarity	NPC4341
0.6571	Remote Similarity	NPC479047
0.6571	Remote Similarity	NPC291638
0.6528	Remote Similarity	NPC41481
0.6389	Remote Similarity	NPC171207
0.6351	Remote Similarity	NPC210591
0.6338	Remote Similarity	NPC90257
0.6338	Remote Similarity	NPC483845
0.6338	Remote Similarity	NPC69357
0.6301	Remote Similarity	NPC479044
0.6267	Remote Similarity	NPC475652
0.625	Remote Similarity	NPC483842
0.6133	Remote Similarity	NPC184747
0.6111	Remote Similarity	NPC191082
0.6087	Remote Similarity	NPC473081
0.6087	Remote Similarity	NPC195647
0.6081	Remote Similarity	NPC306146
0.6081	Remote Similarity	NPC483841
0.6081	Remote Similarity	NPC483844
0.5974	Remote Similarity	NPC483849
0.5972	Remote Similarity	NPC163087
0.5926	Remote Similarity	NPC473115
0.5897	Remote Similarity	NPC475039
0.5867	Remote Similarity	NPC92293
0.5844	Remote Similarity	NPC483848
0.5811	Remote Similarity	NPC27377
0.5775	Remote Similarity	NPC475429
0.5775	Remote Similarity	NPC211137
0.5775	Remote Similarity	NPC66761
0.5775	Remote Similarity	NPC483843
0.5775	Remote Similarity	NPC476094
0.5696	Remote Similarity	NPC476035
0.5634	Remote Similarity	NPC200592
0.5634	Remote Similarity	NPC270498
0.5634	Remote Similarity	NPC610542
0.5616	Remote Similarity	NPC475759
0.5616	Remote Similarity	NPC483847
0.56	Remote Similarity	NPC147217
0.5526	Remote Similarity	NPC473758
0.5526	Remote Similarity	NPC473673
0.5513	Remote Similarity	NPC70716
0.5513	Remote Similarity	NPC97667
0.5513	Remote Similarity	NPC96903
0.5467	Remote Similarity	NPC483883
0.5467	Remote Similarity	NPC151585
0.5405	Remote Similarity	NPC311175
0.5405	Remote Similarity	NPC470152
0.5375	Remote Similarity	NPC479042
0.5316	Remote Similarity	NPC95265
0.525	Remote Similarity	NPC473613
0.525	Remote Similarity	NPC473112
0.5238	Remote Similarity	NPC6576
0.5176	Remote Similarity	NPC75600
0.5176	Remote Similarity	NPC483884
0.5139	Remote Similarity	NPC147561
0.5063	Remote Similarity	NPC472574
0.5062	Remote Similarity	NPC473085
0.5062	Remote Similarity	NPC607428

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC48017 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3106
0.1-0.2	5824
0.2-0.3	219
0.3-0.4	1
0.4-0.5	0
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