NPASS Compound

Natural Product: NPC611341

Natural Product ID	NPC611341
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	JAQJQYMDHBSCKO-YAWJYSLYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL5094991
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic 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 2D 82 87 0 0 0 0 0 0 0 0999 V2000 -4.5729 5.2393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0836 5.4184 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4941 6.7977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1839 4.2182 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6463 3.8844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0884 2.4510 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9941 1.2553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0682 1.3515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3768 4.6875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0183 5.2384 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1179 6.2587 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2175 7.2789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3171 8.2992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4166 9.3194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5162 10.3397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6158 11.3600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7154 12.3802 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8149 13.4005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.9145 14.4207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1974 3.7491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1636 3.1186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6058 1.6852 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4330 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4330 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4120 -1.9894 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2569 -3.2287 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6058 -1.6852 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4330 -2.6205 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0682 -1.3515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0812 -0.2218 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1523 -2.3880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9510 -3.8745 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4732 -1.6772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8247 -2.3281 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2054 -0.2013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7190 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1592 4.8931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4726 6.4395 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4787 4.0436 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9045 8.1770 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8734 7.3872 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0131 6.5594 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1463 3.8881 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0813 5.3199 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4967 2.9675 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2682 0.4637 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1898 2.1610 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0531 0.0872 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1382 5.1591 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0976 7.3582 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1972 8.3785 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2377 6.1793 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3373 7.1996 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2968 9.3988 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3964 10.4190 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4369 8.2199 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5365 9.2401 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4959 11.4393 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5955 12.4595 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6360 10.2604 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7356 11.2806 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6951 13.4798 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7947 14.5001 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.8352 12.3009 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 11.0141 15.4410 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.9348 13.3212 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8943 15.5203 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0340 2.1317 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5410 2.8580 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9913 -0.6422 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5861 -3.1091 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6513 -1.1444 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7528 -3.1166 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2566 -3.0367 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6566 -4.1037 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5852 -0.3302 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1761 -2.9789 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4755 -0.9766 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1739 -3.6795 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3664 0.7484 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2460 -1.4044 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 4 2 1 1 4 5 1 0 5 6 1 0 6 7 1 0 6 8 1 0 8 9 1 6 9 10 1 0 10 11 1 1 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 1 0 10 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 1 26 27 1 0 25 28 1 0 28 29 1 0 28 30 1 0 30 31 1 1 30 32 1 0 32 33 2 0 32 34 1 0 34 35 1 0 34 36 2 0 36 37 1 0 10 38 1 0 21 4 1 0 25 23 1 0 37 30 1 0 38 4 1 0 22 8 1 0 37 8 1 0 1 39 1 0 1 40 1 0 3 41 1 0 3 42 1 0 3 43 1 0 5 44 1 0 5 45 1 0 6 46 1 1 7 47 1 0 7 48 1 0 7 49 1 0 11 50 1 0 11 51 1 0 12 52 1 0 12 53 1 0 13 54 1 0 13 55 1 0 14 56 1 0 14 57 1 0 15 58 1 0 15 59 1 0 16 60 1 0 16 61 1 0 17 62 1 0 17 63 1 0 18 64 1 0 18 65 1 0 19 66 1 0 19 67 1 0 19 68 1 0 21 69 1 1 22 70 1 1 23 71 1 1 26 72 1 0 26 73 1 0 27 74 1 0 28 75 1 6 29 76 1 0 31 77 1 0 35 78 1 0 35 79 1 0 35 80 1 0 36 81 1 0 37 82 1 6 M END

Standard InCHIKey	JAQJQYMDHBSCKO-YAWJYSLYSA-N
Standard InCHI	InChI=1S/C30H44O8/c1-6-7-8-9-10-11-12-13-28-36-23-21-24-27(16-31,35-24)25(33)29(34)20(14-18(4)22(29)32)30(21,38-28)19(5)15-26(23,37-28)17(2)3/h14,19-21,23-25,31,33-34H,2,6-13,15-16H2,1,3-5H3/t19-,20-,21-,23-,24+,25-,26-,27+,28+,29-,30+/m1/s1
SMILES	C=C(C)[C@]12C[C@@H](C)[C@@]34O[C@@](CCCCCCCCC)(O[C@@H]1[C@@H]3[C@@H]1O[C@]1(CO)[C@@H](O)[C@]1(O)C(=O)C(C)=C[C@H]14)O2

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
NPO19812	Pimelea simplex	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21049973]
NPO4278	Wikstroemia monticola	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO19812	Pimelea simplex	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO59121	Stellera chamaejasme L.	Genus	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4278	Wikstroemia monticola	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19812	Pimelea simplex	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19812	Pimelea simplex	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4278	Wikstroemia monticola	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4278	Wikstroemia monticola	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19812	Pimelea simplex	Species	Thymelaeaceae	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
EC50	1

Activity Type	# Activity
Organism	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
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	=	9.0	nM	PMID[35113551]

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 NPC611341 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	15833
0.1-0.2	32472
0.2-0.3	1438
0.3-0.4	30
0.4-0.5	38
0.5-0.6	29
0.6-0.7	14
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC475273
1.0	High Similarity	NPC168849
1.0	High Similarity	NPC217901
0.726	Intermediate Similarity	NPC162495
0.6974	Remote Similarity	NPC474508
0.6974	Remote Similarity	NPC473485
0.6974	Remote Similarity	NPC171411
0.6974	Remote Similarity	NPC485701
0.6842	Remote Similarity	NPC251564
0.6842	Remote Similarity	NPC477189
0.6486	Remote Similarity	NPC608985
0.6463	Remote Similarity	NPC605479
0.64	Remote Similarity	NPC605473
0.64	Remote Similarity	NPC610597
0.6316	Remote Similarity	NPC142882
0.6316	Remote Similarity	NPC608716
0.6316	Remote Similarity	NPC609033
0.6136	Remote Similarity	NPC486154
0.5663	Remote Similarity	NPC180902
0.5581	Remote Similarity	NPC475139
0.5529	Remote Similarity	NPC182266
0.5529	Remote Similarity	NPC475154
0.5529	Remote Similarity	NPC485700
0.5476	Remote Similarity	NPC485693
0.5432	Remote Similarity	NPC329008
0.5432	Remote Similarity	NPC317635
0.5432	Remote Similarity	NPC146310
0.5432	Remote Similarity	NPC485696
0.5412	Remote Similarity	NPC223356
0.5412	Remote Similarity	NPC298697
0.5412	Remote Similarity	NPC475500
0.5412	Remote Similarity	NPC100017
0.5412	Remote Similarity	NPC481742
0.5357	Remote Similarity	NPC475314
0.5357	Remote Similarity	NPC102997
0.5349	Remote Similarity	NPC75831
0.5349	Remote Similarity	NPC471137
0.5287	Remote Similarity	NPC471136
0.5287	Remote Similarity	NPC116727
0.5287	Remote Similarity	NPC39509
0.5227	Remote Similarity	NPC481744
0.5227	Remote Similarity	NPC481743
0.5176	Remote Similarity	NPC324104
0.5176	Remote Similarity	NPC473548
0.5119	Remote Similarity	NPC475606
0.5111	Remote Similarity	NPC475548
0.5111	Remote Similarity	NPC485698

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC611341 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6253
0.1-0.2	2869
0.2-0.3	27
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