NPASS Compound

Natural Product: NPC607068

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 35 37 0 0 0 0 0 0 0 0999 V2000 6.2114 0.3966 0.9894 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3098 -0.6747 1.0709 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9891 -0.5923 0.6481 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1200 -1.6584 0.7373 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8025 -1.5333 0.3014 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3278 -0.3524 -0.2282 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0733 -0.2466 -0.6828 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4255 1.1887 -0.9457 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8604 1.3954 -1.1843 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3423 2.2517 -1.9608 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8048 0.5402 -0.4641 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1735 0.8270 -0.4947 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5902 1.9374 -1.2241 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0482 0.0122 0.1884 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5946 -1.0784 0.8992 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5104 -1.8891 1.5845 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2421 -1.3460 0.9183 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3210 -0.5438 0.2384 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9664 -0.8204 0.2635 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2077 0.7071 -0.3120 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5212 0.6077 0.1142 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0896 0.8282 -0.0477 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2704 0.0723 1.0402 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0308 1.1902 1.7406 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4873 -2.6017 1.1567 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1857 -2.4151 0.4058 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1880 -0.8538 -1.6200 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1692 1.5487 -1.8117 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1631 1.7609 -0.0100 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6640 2.8596 -0.7963 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1069 0.2615 0.1454 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8106 -2.7426 1.0878 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8899 -2.1991 1.4747 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8908 1.6782 -0.7255 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1621 1.4841 0.0191 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 12 14 1 0 14 15 2 0 15 16 1 0 15 17 1 0 17 18 2 0 18 19 1 0 6 20 1 0 20 21 2 0 21 3 1 0 19 7 1 0 18 11 1 0 1 22 1 0 1 23 1 0 1 24 1 0 4 25 1 0 5 26 1 0 7 27 1 0 8 28 1 0 8 29 1 0 13 30 1 0 14 31 1 0 16 32 1 0 17 33 1 0 20 34 1 0 21 35 1 0 M END

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

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

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

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 NPC607068 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	26011
0.1-0.2	19195
0.2-0.3	3703
0.3-0.4	638
0.4-0.5	192
0.5-0.6	66
0.6-0.7	25
0.7-0.8	3
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC274784
1.0	High Similarity	NPC20709
0.7872	Intermediate Similarity	NPC32441
0.7872	Intermediate Similarity	NPC243083
0.7872	Intermediate Similarity	NPC13768
0.7872	Intermediate Similarity	NPC287246
0.7872	Intermediate Similarity	NPC79943
0.78	Intermediate Similarity	NPC302950
0.7551	Intermediate Similarity	NPC338131
0.75	Intermediate Similarity	NPC6407
0.75	Intermediate Similarity	NPC545184
0.7292	Intermediate Similarity	NPC182421
0.717	Intermediate Similarity	NPC236637
0.7059	Intermediate Similarity	NPC321011
0.7059	Intermediate Similarity	NPC294852
0.7059	Intermediate Similarity	NPC188679
0.7018	Intermediate Similarity	NPC108456
0.6939	Remote Similarity	NPC188243
0.6939	Remote Similarity	NPC110228
0.68	Remote Similarity	NPC295261
0.68	Remote Similarity	NPC296490
0.6786	Remote Similarity	NPC477841
0.6667	Remote Similarity	NPC20354
0.6604	Remote Similarity	NPC469758
0.6538	Remote Similarity	NPC287789
0.6538	Remote Similarity	NPC107586
0.6538	Remote Similarity	NPC329203
0.6538	Remote Similarity	NPC222342
0.6471	Remote Similarity	NPC12296
0.6379	Remote Similarity	NPC17170
0.6346	Remote Similarity	NPC150648
0.625	Remote Similarity	NPC26195
0.6226	Remote Similarity	NPC73028
0.614	Remote Similarity	NPC258630
0.6111	Remote Similarity	NPC44721
0.6111	Remote Similarity	NPC211466
0.6111	Remote Similarity	NPC605332
0.6102	Remote Similarity	NPC109223
0.6102	Remote Similarity	NPC10937
0.6038	Remote Similarity	NPC162869
0.6	Remote Similarity	NPC18727
0.6	Remote Similarity	NPC310135
0.5968	Remote Similarity	NPC312973
0.5968	Remote Similarity	NPC200761
0.5968	Remote Similarity	NPC475790
0.5873	Remote Similarity	NPC473990
0.5873	Remote Similarity	NPC611447
0.5849	Remote Similarity	NPC20560
0.5818	Remote Similarity	NPC606248
0.5769	Remote Similarity	NPC265871
0.5769	Remote Similarity	NPC205093
0.5738	Remote Similarity	NPC106976
0.5714	Remote Similarity	NPC475184
0.5692	Remote Similarity	NPC473272
0.5672	Remote Similarity	NPC475784
0.5667	Remote Similarity	NPC271741
0.5667	Remote Similarity	NPC148757
0.566	Remote Similarity	NPC225153
0.566	Remote Similarity	NPC479876
0.5645	Remote Similarity	NPC174953
0.5636	Remote Similarity	NPC255106
0.5636	Remote Similarity	NPC235165
0.5636	Remote Similarity	NPC296917
0.5636	Remote Similarity	NPC156057
0.5636	Remote Similarity	NPC324386
0.5636	Remote Similarity	NPC170907
0.5574	Remote Similarity	NPC477840
0.5556	Remote Similarity	NPC134783
0.549	Remote Similarity	NPC99854
0.5472	Remote Similarity	NPC140890
0.5469	Remote Similarity	NPC470890
0.5455	Remote Similarity	NPC312391
0.5455	Remote Similarity	NPC37392
0.5441	Remote Similarity	NPC227579
0.5441	Remote Similarity	NPC214166
0.5385	Remote Similarity	NPC69531
0.5373	Remote Similarity	NPC64915
0.5357	Remote Similarity	NPC300668
0.5357	Remote Similarity	NPC194432
0.5357	Remote Similarity	NPC482119
0.5357	Remote Similarity	NPC482120
0.5352	Remote Similarity	NPC602605
0.5303	Remote Similarity	NPC118256
0.5294	Remote Similarity	NPC219163
0.5294	Remote Similarity	NPC474038
0.5283	Remote Similarity	NPC329225
0.5283	Remote Similarity	NPC147686
0.5273	Remote Similarity	NPC36016
0.5273	Remote Similarity	NPC204515
0.5273	Remote Similarity	NPC603284
0.5263	Remote Similarity	NPC469764
0.5263	Remote Similarity	NPC475267
0.5238	Remote Similarity	NPC134171
0.5224	Remote Similarity	NPC474021
0.5205	Remote Similarity	NPC158188
0.5185	Remote Similarity	NPC135616
0.5172	Remote Similarity	NPC601395
0.5167	Remote Similarity	NPC484335
0.5156	Remote Similarity	NPC85121
0.5152	Remote Similarity	NPC88964
0.5147	Remote Similarity	NPC279650
0.5139	Remote Similarity	NPC479054
0.5091	Remote Similarity	NPC476480
0.5091	Remote Similarity	NPC213322
0.5091	Remote Similarity	NPC84585
0.5088	Remote Similarity	NPC480993
0.5079	Remote Similarity	NPC470133
0.5079	Remote Similarity	NPC470135

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC607068 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4472
0.1-0.2	4506
0.2-0.3	153
0.3-0.4	11
0.4-0.5	4
0.5-0.6	1
0.6-0.7	0
0.7-0.8	3
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
0.7872	Intermediate Similarity	NPD1550	Phase 2
0.7872	Intermediate Similarity	NPD1552	Clinical (unspecified phase)
0.78	Intermediate Similarity	NPD1934	Phase 0
0.5283	Remote Similarity	NPD1549	Phase 2

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