NPASS Compound

Natural Product: NPC610133

Natural Product ID	NPC610133
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	WWFVAIXZPACOBJ-NRFANRHFSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3787270
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 3D 59 61 0 0 0 0 0 0 0 0999 V2000 5.7073 -0.1910 1.2432 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3333 -0.6400 -0.1157 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2889 -0.2606 -1.2265 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2468 -1.3234 -0.3624 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2881 -1.7113 0.6902 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9136 -1.2498 0.4387 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4856 0.0506 0.6048 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4453 0.9534 1.0303 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1901 0.4433 0.3666 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1520 1.8747 0.5592 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2778 2.7309 -0.5393 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0296 3.7723 -0.3864 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5222 4.1915 0.9363 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4462 4.6174 -1.5666 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7157 -0.4806 -0.0499 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3321 -1.8019 -0.2323 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9744 -2.1749 0.0129 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2817 -3.5219 -0.1927 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3536 -2.7317 -0.6902 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2328 -3.9347 -0.3757 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4787 -2.2093 -1.5016 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9230 -0.8315 -1.0918 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2862 -0.8717 -0.4659 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4154 -0.5896 -1.2038 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6775 -0.6356 -0.6357 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8586 -0.9663 0.6963 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1348 -1.0113 1.2628 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7297 -1.2479 1.4331 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9028 -1.5813 2.7724 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4593 -1.2015 0.8600 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0097 -0.1325 -0.2947 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7828 0.1548 1.2725 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6263 -1.0977 1.9151 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0737 0.6279 1.6239 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7777 -0.2293 -2.1955 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7891 0.6881 -0.9764 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0587 -1.0837 -1.2972 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0353 -1.6219 -1.3809 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3257 -2.8237 0.7537 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6434 -1.3597 1.7014 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1011 1.3713 0.3844 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2435 1.9518 0.7437 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3097 2.1364 1.5564 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0574 2.4716 -1.5362 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7698 4.0573 1.7616 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8504 5.2707 0.9134 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4339 3.6456 1.2674 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5129 4.3729 -1.7678 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4246 5.6637 -1.2229 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7787 4.4549 -2.4332 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3423 -4.0975 0.6389 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3530 -2.9009 -1.3233 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2589 -2.2744 -2.5980 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0270 -0.2311 -2.0441 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2780 -0.3254 -2.2605 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5671 -0.4153 -1.2059 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.6042 -1.9290 1.2182 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4425 -2.3854 3.0670 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5740 -1.4259 1.4485 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 2 3 4 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 7 9 1 0 9 10 1 0 10 11 1 0 11 12 2 3 12 13 1 0 12 14 1 0 9 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 16 19 1 0 19 20 2 0 19 21 1 0 21 22 1 0 22 23 1 0 23 24 2 0 24 25 1 0 25 26 2 0 26 27 1 0 26 28 1 0 28 29 1 0 28 30 2 0 22 31 1 0 17 6 1 0 30 23 1 0 31 15 1 0 1 32 1 0 1 33 1 0 1 34 1 0 3 35 1 0 3 36 1 0 3 37 1 0 4 38 1 0 5 39 1 0 5 40 1 0 8 41 1 0 10 42 1 0 10 43 1 0 11 44 1 0 13 45 1 0 13 46 1 0 13 47 1 0 14 48 1 0 14 49 1 0 14 50 1 0 18 51 1 0 21 52 1 0 21 53 1 0 22 54 1 6 24 55 1 0 25 56 1 0 27 57 1 0 29 58 1 0 30 59 1 0 M END

Standard InCHIKey	WWFVAIXZPACOBJ-NRFANRHFSA-N
Standard InCHI	InChI=1S/C25H28O6/c1-13(2)5-8-16-23(29)17(9-6-14(3)4)25-22(24(16)30)20(28)12-21(31-25)15-7-10-18(26)19(27)11-15/h5-7,10-11,21,26-27,29-30H,8-9,12H2,1-4H3/t21-/m0/s1
SMILES	CC(C)=CCc1c(O)c(CC=C(C)C)c2c(c1O)C(=O)C[C@@H](c1ccc(O)c(O)c1)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
NPO8046	Muntingia calabura	Species	Muntingiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[2045815]
NPO8046	Muntingia calabura	Species	Muntingiaceae	Eukaryota	n.a.	root	n.a.	PMID[2045815]
NPO19912	Vellozia nanuzae	Species	Velloziaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO19487	Dorstenia mannii	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8046	Muntingia calabura	Species	Muntingiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO50053	Vellozia coronata	Genus	Velloziaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8046	Muntingia calabura	Species	Muntingiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8046	Muntingia calabura	Species	Muntingiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19487	Dorstenia mannii	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19487	Dorstenia mannii	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19912	Vellozia nanuzae	Species	Velloziaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8046	Muntingia calabura	Species	Muntingiaceae	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	1
Ratio CC50/IC50	1
CC50	1

Activity Type	# Activity
Unchecked	1
Organism	1
Non-molecular	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
NPT28438	Unchecked	Unchecked	n.a.	Ratio CC50/IC50	=	1.58	n.a.	PMID[26906638]
NPT634	Organism	Leishmania amazonensis	Leishmania amazonensis	IC50	=	29200.0	nM	PMID[26906638]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	CC50	=	46270.0	nM	PMID[26906638]

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 NPC610133 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	18778
0.1-0.2	26506
0.2-0.3	3857
0.3-0.4	508
0.4-0.5	148
0.5-0.6	44
0.6-0.7	7
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
0.8393	Intermediate Similarity	NPC265040
0.7966	Intermediate Similarity	NPC608140
0.7759	Intermediate Similarity	NPC187282
0.7213	Intermediate Similarity	NPC285555
0.6364	Remote Similarity	NPC473078
0.6324	Remote Similarity	NPC484416
0.619	Remote Similarity	NPC107572
0.619	Remote Similarity	NPC32739
0.6	Remote Similarity	NPC66515
0.6	Remote Similarity	NPC213896
0.6	Remote Similarity	NPC192083
0.5942	Remote Similarity	NPC246948
0.5846	Remote Similarity	NPC250214
0.5846	Remote Similarity	NPC75049
0.5821	Remote Similarity	NPC291878
0.5811	Remote Similarity	NPC283234
0.5781	Remote Similarity	NPC76372
0.5781	Remote Similarity	NPC37496
0.5758	Remote Similarity	NPC197252
0.5758	Remote Similarity	NPC254412
0.5753	Remote Similarity	NPC192686
0.5672	Remote Similarity	NPC125855
0.5652	Remote Similarity	NPC138288
0.5616	Remote Similarity	NPC261063
0.5606	Remote Similarity	NPC69674
0.5606	Remote Similarity	NPC148757
0.5541	Remote Similarity	NPC321779
0.5538	Remote Similarity	NPC164980
0.5522	Remote Similarity	NPC480990
0.5467	Remote Similarity	NPC119209
0.5455	Remote Similarity	NPC1089
0.5455	Remote Similarity	NPC324436
0.5455	Remote Similarity	NPC78
0.5455	Remote Similarity	NPC236766
0.5455	Remote Similarity	NPC150408
0.5455	Remote Similarity	NPC306829
0.5405	Remote Similarity	NPC228779
0.5405	Remote Similarity	NPC483811
0.5373	Remote Similarity	NPC95936
0.5352	Remote Similarity	NPC35038
0.5333	Remote Similarity	NPC284820
0.5294	Remote Similarity	NPC220998
0.5294	Remote Similarity	NPC310130
0.5286	Remote Similarity	NPC161506
0.5278	Remote Similarity	NPC166934
0.5278	Remote Similarity	NPC142405
0.527	Remote Similarity	NPC214774
0.5217	Remote Similarity	NPC223500
0.5217	Remote Similarity	NPC76338
0.5217	Remote Similarity	NPC250242
0.5147	Remote Similarity	NPC149026
0.5143	Remote Similarity	NPC182852
0.5075	Remote Similarity	NPC1486
0.507	Remote Similarity	NPC36217
0.5065	Remote Similarity	NPC312273

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC610133 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3204
0.1-0.2	5827
0.2-0.3	112
0.3-0.4	6
0.4-0.5	0
0.5-0.6	0
0.6-0.7	1
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
0.6	Remote Similarity	NPD2393	Clinical (unspecified phase)

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