NPASS Compound

Natural Product: NPC601739

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 83 87 0 0 0 0 0 0 0 0999 V2000 5.3457 1.8699 -1.7250 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9862 1.5087 -0.2981 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5680 2.5713 0.6132 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6655 0.2061 0.0238 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7939 -0.8947 -0.4920 C 0 0 1 0 0 0 0 0 0 0 0 0 5.4198 -2.1451 -0.4656 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6109 -0.9872 0.4902 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2686 -1.4824 1.7929 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7720 -2.1055 -0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4190 -2.0440 0.6336 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7294 -0.8287 -0.0037 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8797 -0.9646 -1.4739 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4880 0.3293 0.5865 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8532 1.3875 1.0682 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6247 1.5665 1.0909 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2414 0.5669 0.1342 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7213 0.7537 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.2771 1.3152 1.2509 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9917 1.8323 -1.0695 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4496 2.1004 -1.1169 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3731 0.9429 -1.1489 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.5130 1.3183 -0.3844 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8523 -0.3791 -0.7591 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1503 -1.3519 -1.9290 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5950 -1.0341 0.3947 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9447 -1.2349 0.0930 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3772 -0.4599 -0.5698 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9399 -1.7380 0.0928 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4679 -1.8760 -0.2533 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7296 -0.7775 0.4492 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6706 -1.1428 1.9116 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9789 0.3342 0.6691 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4882 1.4367 -0.2097 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6506 0.9867 -2.3241 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4761 2.3255 -2.2623 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1961 2.5850 -1.7641 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5843 2.2280 1.6715 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6236 2.7423 0.3302 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0329 3.5365 0.5311 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6461 0.1314 -0.5300 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9030 0.1514 1.0874 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4499 -0.6286 -1.5058 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2704 -2.1036 -0.9935 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1571 -2.0835 1.5971 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5110 -0.5909 2.4369 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5323 -2.0705 2.3772 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2270 -3.0859 0.3243 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7497 -2.1833 -1.1125 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6147 -1.8280 1.7254 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8874 -2.9721 0.4593 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8256 -0.5296 -1.8552 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0760 -0.5062 -2.0862 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8144 -2.0643 -1.7325 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4551 2.2156 1.4920 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8716 2.5863 0.6716 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0367 1.4608 2.1159 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8019 0.8568 -0.8700 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3321 1.5859 1.2572 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7471 2.3050 1.4099 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0848 0.7491 2.1729 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4622 2.7446 -0.7983 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6787 1.4386 -2.0738 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5991 2.7637 -2.0283 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7058 2.8336 -0.2910 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8170 0.9164 -2.1941 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3699 2.1357 0.1155 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4684 -1.1787 -2.7618 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1846 -1.1051 -2.2474 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1767 -2.3953 -1.5634 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1997 -2.0508 0.6095 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4952 -0.4861 1.3521 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4331 -1.1911 0.9439 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9306 -0.5385 -1.6134 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1376 -1.7821 1.1656 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4720 -2.5728 -0.4012 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4091 -1.7004 -1.3628 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0797 -2.8715 -0.0691 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3652 -2.2332 1.9301 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6315 -1.1247 2.4279 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0526 -0.5256 2.4727 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2269 0.6818 1.7221 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0026 1.4389 -1.1905 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1770 2.4092 0.2773 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 1 0 5 7 1 0 7 8 1 1 7 9 1 0 9 10 1 0 10 11 1 0 11 12 1 6 11 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 1 17 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 21 23 1 0 23 24 1 6 23 25 1 0 25 26 1 0 23 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 1 13 32 1 0 32 33 1 0 33 2 1 0 32 7 1 0 30 11 1 0 30 16 1 0 27 17 1 0 1 34 1 0 1 35 1 0 1 36 1 0 3 37 1 0 3 38 1 0 3 39 1 0 4 40 1 0 4 41 1 0 5 42 1 6 6 43 1 0 8 44 1 0 8 45 1 0 8 46 1 0 9 47 1 0 9 48 1 0 10 49 1 0 10 50 1 0 12 51 1 0 12 52 1 0 12 53 1 0 14 54 1 0 15 55 1 0 15 56 1 0 16 57 1 6 18 58 1 0 18 59 1 0 18 60 1 0 19 61 1 0 19 62 1 0 20 63 1 0 20 64 1 0 21 65 1 6 22 66 1 0 24 67 1 0 24 68 1 0 24 69 1 0 25 70 1 0 25 71 1 0 26 72 1 0 27 73 1 6 28 74 1 0 28 75 1 0 29 76 1 0 29 77 1 0 31 78 1 0 31 79 1 0 31 80 1 0 32 81 1 1 33 82 1 0 33 83 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 NPC601739 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	27989
0.1-0.2	18591
0.2-0.3	2451
0.3-0.4	628
0.4-0.5	146
0.5-0.6	36
0.6-0.7	11
0.7-0.8	0
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	NPC230295
1.0	High Similarity	NPC98386
0.7544	Intermediate Similarity	NPC196753
0.6949	Remote Similarity	NPC34177
0.6825	Remote Similarity	NPC213412
0.6667	Remote Similarity	NPC311078
0.6452	Remote Similarity	NPC253402
0.6393	Remote Similarity	NPC101475
0.619	Remote Similarity	NPC53744
0.6167	Remote Similarity	NPC290598
0.6167	Remote Similarity	NPC30590
0.6032	Remote Similarity	NPC253807
0.6032	Remote Similarity	NPC158662
0.6032	Remote Similarity	NPC478657
0.5942	Remote Similarity	NPC263393
0.5781	Remote Similarity	NPC235341
0.5735	Remote Similarity	NPC270768
0.5735	Remote Similarity	NPC59263
0.5735	Remote Similarity	NPC210106
0.5696	Remote Similarity	NPC224121
0.5692	Remote Similarity	NPC238992
0.5634	Remote Similarity	NPC294360
0.5522	Remote Similarity	NPC246708
0.5513	Remote Similarity	NPC237503
0.5507	Remote Similarity	NPC7260
0.5507	Remote Similarity	NPC210037
0.5507	Remote Similarity	NPC229281
0.5507	Remote Similarity	NPC120968
0.5507	Remote Similarity	NPC121798
0.5507	Remote Similarity	NPC234346
0.5507	Remote Similarity	NPC227467
0.5507	Remote Similarity	NPC273621
0.5493	Remote Similarity	NPC191412
0.5493	Remote Similarity	NPC114159
0.5493	Remote Similarity	NPC6818
0.5455	Remote Similarity	NPC159168
0.5429	Remote Similarity	NPC61543
0.5429	Remote Similarity	NPC293048
0.5429	Remote Similarity	NPC225585
0.5342	Remote Similarity	NPC116457
0.5333	Remote Similarity	NPC258547
0.5205	Remote Similarity	NPC127689
0.5205	Remote Similarity	NPC130520
0.5156	Remote Similarity	NPC27765
0.5156	Remote Similarity	NPC122418
0.5156	Remote Similarity	NPC491014
0.5075	Remote Similarity	NPC40394
0.5075	Remote Similarity	NPC480924
0.507	Remote Similarity	NPC488519
0.5068	Remote Similarity	NPC480919

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC601739 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8169
0.1-0.2	944
0.2-0.3	34
0.3-0.4	2
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
0.6719	Remote Similarity	NPD7645	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