NPASS Compound

Natural Product: NPC611909

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 51 54 0 0 0 0 0 0 0 0999 V2000 6.2510 1.1694 -1.5004 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7277 0.3012 -0.4948 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3929 0.4812 -0.1574 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5832 1.4364 -0.7393 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2588 1.5998 -0.3906 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7068 0.7895 0.5710 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4938 -0.1571 1.1536 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8355 -0.3296 0.8069 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6131 -1.2998 1.4146 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0252 -2.1266 2.4055 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2704 0.9976 0.9172 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3155 -0.2160 1.5903 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7353 -0.4680 1.2750 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6667 -0.9404 2.2101 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9705 -1.1530 1.8154 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3730 -0.9079 0.5132 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6738 -1.1102 0.0803 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6880 -1.5772 0.9187 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4189 -0.4342 -0.4050 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7625 -0.1711 -1.7209 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6333 -1.2389 -2.6461 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1272 -0.2209 -0.0231 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1081 0.2811 -0.9548 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4372 1.3463 -0.2466 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0106 2.4306 -1.0247 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4856 2.6500 -1.0703 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3542 1.0799 -1.5657 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7983 0.9746 -2.4864 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0571 2.2453 -1.2475 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0106 2.0752 -1.4947 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1020 -0.8038 1.9054 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1366 -2.6081 1.9070 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7466 -2.8935 2.7600 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7090 -1.5371 3.2985 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1724 1.8272 1.6591 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1026 -0.2239 2.6798 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2331 -1.1253 1.1976 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3432 -1.1282 3.2221 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6923 -1.5172 2.5342 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6855 -1.0548 1.9193 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6978 -1.3851 0.5040 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5936 -2.6635 1.1760 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1180 -2.1191 -2.1604 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0721 -1.0086 -3.6344 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5475 -1.4795 -2.7149 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5294 0.6821 -1.8957 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3805 -0.5303 -1.2168 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4695 3.3797 -0.6430 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4176 2.3264 -2.0657 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7690 3.6307 -0.5963 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8159 2.7248 -2.1265 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 2 0 8 9 1 0 9 10 1 0 6 11 1 0 11 12 1 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 1 0 16 19 1 0 19 20 1 0 20 21 1 0 19 22 2 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 8 3 1 0 24 11 1 0 26 5 1 0 22 13 1 0 1 27 1 0 1 28 1 0 1 29 1 0 4 30 1 0 7 31 1 0 10 32 1 0 10 33 1 0 10 34 1 0 11 35 1 1 12 36 1 0 12 37 1 0 14 38 1 0 15 39 1 0 18 40 1 0 18 41 1 0 18 42 1 0 21 43 1 0 21 44 1 0 21 45 1 0 23 46 1 0 23 47 1 0 25 48 1 0 25 49 1 0 26 50 1 0 26 51 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 NPC611909 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	33314
0.1-0.2	15336
0.2-0.3	951
0.3-0.4	193
0.4-0.5	21
0.5-0.6	18
0.6-0.7	10
0.7-0.8	0
0.8-0.85	1
0.85-0.9	3
0.9-0.95	0
0.95-1	4

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC210437
1.0	High Similarity	NPC16107
1.0	High Similarity	NPC106295
0.9787	High Similarity	NPC51957
0.8654	High Similarity	NPC216459
0.8654	High Similarity	NPC41178
0.8654	High Similarity	NPC138487
0.8148	Intermediate Similarity	NPC326205
0.75	Intermediate Similarity	NPC204828
0.75	Intermediate Similarity	NPC295691
0.75	Intermediate Similarity	NPC207757
0.75	Intermediate Similarity	NPC54379
0.75	Intermediate Similarity	NPC5238
0.7455	Intermediate Similarity	NPC31311
0.7455	Intermediate Similarity	NPC234392
0.7069	Intermediate Similarity	NPC264850
0.6964	Remote Similarity	NPC39701
0.6964	Remote Similarity	NPC184026
0.6863	Remote Similarity	NPC128019
0.6552	Remote Similarity	NPC276588
0.6552	Remote Similarity	NPC127674
0.6552	Remote Similarity	NPC278799
0.6379	Remote Similarity	NPC7467
0.625	Remote Similarity	NPC232514
0.6129	Remote Similarity	NPC606650
0.6	Remote Similarity	NPC469817
0.5781	Remote Similarity	NPC276944
0.5781	Remote Similarity	NPC238530
0.5625	Remote Similarity	NPC2314
0.5484	Remote Similarity	NPC189266
0.5484	Remote Similarity	NPC172765
0.5484	Remote Similarity	NPC2413
0.5484	Remote Similarity	NPC110416
0.5439	Remote Similarity	NPC213206
0.5439	Remote Similarity	NPC188163
0.5439	Remote Similarity	NPC328750
0.541	Remote Similarity	NPC151895
0.5397	Remote Similarity	NPC27887
0.5312	Remote Similarity	NPC312025
0.5303	Remote Similarity	NPC146288
0.5263	Remote Similarity	NPC314682
0.5246	Remote Similarity	NPC153631
0.5156	Remote Similarity	NPC249797
0.5156	Remote Similarity	NPC193949

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC611909 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4659
0.1-0.2	4260
0.2-0.3	201
0.3-0.4	27
0.4-0.5	1
0.5-0.6	1
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	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD4584	Phase 2
0.5439	Remote Similarity	NPD4664	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