NPASS Compound

Natural Product: NPC601607

Natural Product ID	NPC601607
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	GWACEFYEIOPAJV-MIUGBVLSSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL4765046
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 52 56 0 0 0 0 0 0 0 0999 V2000 3.3457 -1.3401 -1.1840 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9378 -0.5818 -0.2625 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7956 0.0509 0.6095 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2266 -0.1601 0.4663 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9669 -0.4066 1.5999 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3303 -0.6104 1.4870 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9648 -0.5721 0.2649 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2016 -0.3233 -0.8564 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8226 -0.1131 -0.7789 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0838 -0.3414 -1.9283 O 0 0 0 0 0 0 0 0 0 0 0 0 9.4251 -0.2716 -1.4307 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3010 -0.7415 -0.1115 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3298 0.8716 1.6046 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0350 1.0532 1.7225 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1761 0.4653 0.9070 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1603 0.6832 1.0670 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1476 0.1140 0.2640 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4606 0.3809 0.4878 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5907 -0.0819 -0.1929 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2832 0.9640 -0.8077 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4977 0.4567 -1.2340 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0614 1.2158 -2.4104 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2640 2.5482 -2.0791 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4312 0.4604 -0.0532 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.5208 -0.3351 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7262 -0.1056 1.1256 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.3813 0.9484 1.9942 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4505 -0.8287 0.7899 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.8063 -2.0449 0.2102 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7117 -0.7108 -0.7389 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6532 -0.9643 -0.9414 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5731 -0.3768 -0.1213 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4630 -0.4357 2.5592 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9200 -0.8065 2.3873 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2424 0.0809 -1.6738 H 0 0 0 0 0 0 0 0 0 0 0 0 9.7151 0.8036 -1.3663 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1044 -0.8734 -2.0460 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0453 1.3546 2.2755 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4990 1.3404 1.8669 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2878 -0.7551 -1.0158 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3533 -0.6017 -1.5421 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3952 1.0694 -3.2741 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0307 0.7461 -2.6655 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8057 3.1192 -2.7385 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7692 1.5092 0.0981 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2910 -0.1683 0.2352 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4254 -0.7707 1.6688 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0773 1.7422 1.5088 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8770 -1.0706 1.7020 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9285 -2.7691 0.8801 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4022 -1.1975 -1.4124 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9768 -1.6199 -1.7406 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 8 10 1 0 10 11 1 0 11 12 1 0 3 13 2 0 13 14 1 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 21 24 1 0 24 25 1 0 24 26 1 0 26 27 1 0 26 28 1 0 28 29 1 0 17 30 2 0 30 31 1 0 31 32 2 0 32 2 1 0 9 4 1 0 32 15 1 0 12 7 1 0 28 19 1 0 5 33 1 0 6 34 1 0 9 35 1 0 11 36 1 0 11 37 1 0 13 38 1 0 16 39 1 0 19 40 1 6 21 41 1 6 22 42 1 0 22 43 1 0 23 44 1 0 24 45 1 1 25 46 1 0 26 47 1 1 27 48 1 0 28 49 1 1 29 50 1 0 30 51 1 0 31 52 1 0 M END

Standard InCHIKey	GWACEFYEIOPAJV-MIUGBVLSSA-N
Standard InCHI	InChI=1S/C22H20O10/c23-7-17-19(25)20(26)21(27)22(32-17)31-11-2-3-12-15(6-11)28-8-13(18(12)24)10-1-4-14-16(5-10)30-9-29-14/h1-6,8,17,19-23,25-27H,7,9H2/t17-,19-,20+,21-,22-/m1/s1
SMILES	O=c1c(-c2ccc3c(c2)OCO3)coc2cc(O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)ccc12

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
NPO22104	Trifolium pratense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/S0031-9422(00)94679-X]
NPO22104	Trifolium pratense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30199256]
NPO6731.1	Ononis spinosa	Under-species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[9182126]
NPO43872	Ormocarpum cochinchinense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12708	Rothia indica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23436	Cladrastis sikokiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO18041	Cladrastis platycarpa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22104	Trifolium pratense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO53541	Thermopsis alterniflora	Genus	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO6731.1	Ononis spinosa	Under-species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22104	Trifolium pratense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22104	Trifolium pratense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22104	Trifolium pratense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18041	Cladrastis platycarpa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22104	Trifolium pratense	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12708	Rothia indica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23436	Cladrastis sikokiana	Species	Fabaceae	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
IC10	1

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
NPT2219	Cell line	C2C12	Mus musculus	IC50	=	13.48	ug.mL-1	PMID[33412152]
NPT2219	Cell line	C2C12	Mus musculus	IC10	=	4.18	ug ml-1	PMID[33412152]

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 NPC601607 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	24296
0.1-0.2	22356
0.2-0.3	2444
0.3-0.4	616
0.4-0.5	107
0.5-0.6	25
0.6-0.7	6
0.7-0.8	1
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
0.7838	Intermediate Similarity	NPC45165
0.7403	Intermediate Similarity	NPC161749
0.725	Intermediate Similarity	NPC229729
0.6753	Remote Similarity	NPC25547
0.6709	Remote Similarity	NPC135345
0.6528	Remote Similarity	NPC602183
0.6341	Remote Similarity	NPC258035
0.622	Remote Similarity	NPC211014
0.6145	Remote Similarity	NPC603782
0.5952	Remote Similarity	NPC105511
0.5882	Remote Similarity	NPC73511
0.5618	Remote Similarity	NPC307518
0.56	Remote Similarity	NPC148497
0.5581	Remote Similarity	NPC197896
0.5581	Remote Similarity	NPC313163
0.5581	Remote Similarity	NPC156457
0.5556	Remote Similarity	NPC48773
0.5556	Remote Similarity	NPC479407
0.5455	Remote Similarity	NPC100720
0.5455	Remote Similarity	NPC205076
0.5412	Remote Similarity	NPC487214
0.5408	Remote Similarity	NPC231194
0.5405	Remote Similarity	NPC185607
0.5402	Remote Similarity	NPC234739
0.5395	Remote Similarity	NPC471590
0.5393	Remote Similarity	NPC224462
0.5385	Remote Similarity	NPC103409
0.5361	Remote Similarity	NPC51326
0.5354	Remote Similarity	NPC235575
0.5316	Remote Similarity	NPC35544
0.5227	Remote Similarity	NPC168822
0.5222	Remote Similarity	NPC479402
0.5055	Remote Similarity	NPC481043
0.5055	Remote Similarity	NPC80140

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC601607 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5260
0.1-0.2	3805
0.2-0.3	74
0.3-0.4	8
0.4-0.5	2
0.5-0.6	0
0.6-0.7	0
0.7-0.8	1
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
0.7403	Intermediate Similarity	NPD4381	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