NPASS Compound

Natural Product: NPC612036

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 49 52 0 0 0 0 0 0 0 0999 V2000 1.1444 -1.4027 -0.9846 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4458 -0.1856 -0.0956 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4438 0.6454 -0.8265 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8215 0.0270 -0.7594 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2492 -0.0611 0.6889 C 0 0 2 0 0 0 0 0 0 0 0 0 5.5355 -0.5773 0.7836 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3127 -0.8660 1.5226 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8847 -0.7158 1.2047 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9809 -1.0650 2.0965 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4777 -0.9759 1.9190 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8764 -0.4788 0.5484 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1464 0.5600 0.1516 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2520 1.3930 -1.0302 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5929 2.0396 -0.7515 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5943 0.9433 -0.6122 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6175 0.0618 -1.8259 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9488 1.3478 -0.2588 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4924 2.3853 -0.5464 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5409 0.2381 0.5268 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3792 -0.7293 0.8009 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2033 0.1666 0.6513 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3674 -1.1494 -1.7165 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0533 -1.6698 -1.5614 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9009 -2.2921 -0.3646 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5214 1.6852 -0.4560 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1512 0.6255 -1.9170 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5118 0.7650 -1.2618 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9255 -0.9060 -1.3101 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2985 0.9927 1.0695 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7484 -0.8036 1.7132 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6098 -1.9517 1.5122 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4755 -0.5570 2.5984 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3310 -1.4561 3.0553 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8718 -0.2892 2.7030 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9181 -1.9774 2.1463 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8941 -1.3525 -0.1266 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3045 1.2058 1.0452 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5327 2.1594 -1.1660 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3765 0.7386 -1.9017 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8669 2.6430 -1.6397 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5776 2.6954 0.1267 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0117 -0.8393 -1.7539 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2569 0.6607 -2.6881 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6731 -0.2199 -2.0654 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9358 0.5616 1.5107 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3245 -0.2596 -0.0734 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3599 -1.4708 -0.0342 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4775 -1.2031 1.7911 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1770 0.9142 1.4693 H 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 5 7 1 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 6 15 17 1 0 17 18 2 0 17 19 1 0 19 20 1 0 20 21 1 0 8 2 1 0 21 11 1 0 12 2 1 0 21 15 1 0 1 22 1 0 1 23 1 0 1 24 1 0 3 25 1 0 3 26 1 0 4 27 1 0 4 28 1 0 5 29 1 1 6 30 1 0 7 31 1 0 7 32 1 0 9 33 1 0 10 34 1 0 10 35 1 0 11 36 1 6 12 37 1 1 13 38 1 0 13 39 1 0 14 40 1 0 14 41 1 0 16 42 1 0 16 43 1 0 16 44 1 0 19 45 1 0 19 46 1 0 20 47 1 0 20 48 1 0 21 49 1 1 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 NPC612036 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	19694
0.1-0.2	25786
0.2-0.3	4085
0.3-0.4	184
0.4-0.5	51
0.5-0.6	43
0.6-0.7	9
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	Natural Product ID
1.0	High Similarity	NPC151519
0.7115	Intermediate Similarity	NPC20688
0.6604	Remote Similarity	NPC221758
0.6481	Remote Similarity	NPC328313
0.6364	Remote Similarity	NPC76879
0.6316	Remote Similarity	NPC33913
0.6316	Remote Similarity	NPC59453
0.6275	Remote Similarity	NPC96319
0.625	Remote Similarity	NPC51014
0.6034	Remote Similarity	NPC472265
0.6034	Remote Similarity	NPC25833
0.5862	Remote Similarity	NPC328351
0.5833	Remote Similarity	NPC243985
0.5833	Remote Similarity	NPC280710
0.5833	Remote Similarity	NPC240650
0.5818	Remote Similarity	NPC162742
0.5818	Remote Similarity	NPC304309
0.5818	Remote Similarity	NPC470228
0.5714	Remote Similarity	NPC22105
0.5714	Remote Similarity	NPC34019
0.5714	Remote Similarity	NPC107059
0.5714	Remote Similarity	NPC600590
0.5614	Remote Similarity	NPC136188
0.5614	Remote Similarity	NPC28657
0.5614	Remote Similarity	NPC474216
0.5614	Remote Similarity	NPC154330
0.5517	Remote Similarity	NPC230301
0.5517	Remote Similarity	NPC113733
0.5517	Remote Similarity	NPC198968
0.5517	Remote Similarity	NPC285893
0.5517	Remote Similarity	NPC134847
0.55	Remote Similarity	NPC318495
0.5469	Remote Similarity	NPC601043
0.5469	Remote Similarity	NPC605412
0.5424	Remote Similarity	NPC241290
0.5424	Remote Similarity	NPC164840
0.5424	Remote Similarity	NPC484739
0.5424	Remote Similarity	NPC209944
0.5424	Remote Similarity	NPC264245
0.5424	Remote Similarity	NPC155986
0.541	Remote Similarity	NPC603646
0.5333	Remote Similarity	NPC328714
0.5333	Remote Similarity	NPC321381
0.5323	Remote Similarity	NPC473943
0.5323	Remote Similarity	NPC155011
0.5246	Remote Similarity	NPC1272
0.5246	Remote Similarity	NPC470614
0.5238	Remote Similarity	NPC47761
0.5238	Remote Similarity	NPC488870
0.5161	Remote Similarity	NPC477522
0.5091	Remote Similarity	NPC139397
0.5085	Remote Similarity	NPC131872
0.5077	Remote Similarity	NPC474349
0.5077	Remote Similarity	NPC474189

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC612036 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6958
0.1-0.2	1940
0.2-0.3	219
0.3-0.4	16
0.4-0.5	8
0.5-0.6	2
0.6-0.7	3
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	NPD3667	Phase 4
0.6604	Remote Similarity	NPD4786	Phase 1
0.6275	Remote Similarity	NPD3701	Pre-clinical
0.6034	Remote Similarity	NPD3668	Pre-clinical
0.5614	Remote Similarity	NPD6942	Phase 4
0.5517	Remote Similarity	NPD7339	Approved

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