NPASS Compound

Natural Product: NPC608477

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 74 79 0 0 0 0 0 0 0 0999 V2000 7.8939 0.1670 -0.0966 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5474 -0.4386 0.1894 C 0 0 1 0 0 0 0 0 0 0 0 0 5.8068 0.3191 1.2852 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3955 -0.2793 1.3134 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7341 0.1044 0.0238 C 0 0 1 0 0 0 0 0 0 0 0 0 4.6592 0.4904 -0.9607 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6466 -0.4803 -1.0142 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9338 -0.8896 -0.5027 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0295 -0.2870 -1.3487 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7644 -1.0952 -1.5452 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3051 -0.2512 -0.9740 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5157 -0.9456 -0.4870 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2348 -1.6243 -1.6122 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5385 -0.9897 -1.9776 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4843 -0.8204 -0.8324 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.3157 0.4356 -1.1292 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4667 0.5808 -0.1823 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.6520 0.0606 -0.6426 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0316 -0.0505 1.1456 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5766 0.3986 1.3381 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7339 -0.5083 0.4706 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5476 -1.8060 1.2560 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4433 0.1140 0.0774 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7982 0.9131 1.1811 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4801 1.4621 0.7624 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4204 0.4229 0.1994 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7402 -0.6135 1.2397 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6133 0.9394 -0.5242 C 0 0 1 0 0 0 0 0 0 0 0 0 2.7838 1.2655 0.3356 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3829 2.5804 -0.1316 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8521 1.0925 -0.6709 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3991 0.3539 0.8592 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4987 -0.6206 -0.6173 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7290 -1.4617 0.6089 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2903 0.2221 2.2649 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7770 1.3838 1.0118 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4910 -1.3605 1.4575 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8932 0.1673 2.2025 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2043 -0.4678 -1.9725 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1170 -1.4757 -0.9795 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4662 0.0272 -2.3190 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8402 -2.1127 -1.1474 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5865 -1.2000 -2.6512 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5976 0.5291 -1.6996 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2186 -1.6857 0.2829 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4044 -2.7203 -1.4051 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5884 -1.6055 -2.5144 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3480 -0.0139 -2.5076 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0295 -1.6342 -2.7309 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1807 -1.6681 -0.6890 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6084 0.4096 -2.1914 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6585 1.3378 -1.0097 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6124 1.6729 0.0660 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2255 0.7962 -0.9999 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1143 -1.1476 1.0873 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6483 0.4058 1.9417 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5347 1.4521 1.0316 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3291 0.2751 2.4229 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7102 -2.6984 0.6081 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5830 -1.8290 1.7926 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3332 -1.8979 2.0608 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6461 0.8283 -0.7606 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7862 0.3760 2.1530 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4819 1.7962 1.3549 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0220 1.9060 1.6580 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6495 2.2445 -0.0017 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0798 -1.5747 0.8072 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5074 -0.2847 1.9450 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1746 -0.8261 1.8100 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2949 1.7607 -1.1857 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5789 1.3636 1.4009 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5569 3.2819 0.7244 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3334 2.3641 -0.6508 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7172 3.0644 -0.8770 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 6 6 7 1 0 5 8 1 0 8 9 1 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 0 16 17 1 0 17 18 1 0 17 19 1 0 19 20 1 0 20 21 1 0 21 22 1 1 21 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 1 26 28 1 0 28 29 1 0 29 30 1 0 7 2 1 0 28 9 1 0 29 5 1 0 26 11 1 0 23 12 1 0 21 15 1 0 1 31 1 0 1 32 1 0 1 33 1 0 2 34 1 1 3 35 1 0 3 36 1 0 4 37 1 0 4 38 1 0 7 39 1 0 7 40 1 0 9 41 1 6 10 42 1 0 10 43 1 0 11 44 1 6 12 45 1 1 13 46 1 0 13 47 1 0 14 48 1 0 14 49 1 0 15 50 1 1 16 51 1 0 16 52 1 0 17 53 1 1 18 54 1 0 19 55 1 0 19 56 1 0 20 57 1 0 20 58 1 0 22 59 1 0 22 60 1 0 22 61 1 0 23 62 1 6 24 63 1 0 24 64 1 0 25 65 1 0 25 66 1 0 27 67 1 0 27 68 1 0 27 69 1 0 28 70 1 6 29 71 1 1 30 72 1 0 30 73 1 0 30 74 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 NPC608477 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	24507
0.1-0.2	23364
0.2-0.3	1655
0.3-0.4	169
0.4-0.5	98
0.5-0.6	38
0.6-0.7	15
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC248944
1.0	High Similarity	NPC7479
1.0	High Similarity	NPC257296
0.8	Intermediate Similarity	NPC481427
0.7797	Intermediate Similarity	NPC296734
0.7627	Intermediate Similarity	NPC227260
0.7619	Intermediate Similarity	NPC161035
0.7619	Intermediate Similarity	NPC170438
0.6613	Remote Similarity	NPC24556
0.6406	Remote Similarity	NPC273290
0.6406	Remote Similarity	NPC232044
0.6389	Remote Similarity	NPC144790
0.6389	Remote Similarity	NPC149400
0.6389	Remote Similarity	NPC88962
0.6364	Remote Similarity	NPC305808
0.6351	Remote Similarity	NPC473774
0.6351	Remote Similarity	NPC481418
0.6351	Remote Similarity	NPC481419
0.6351	Remote Similarity	NPC481417
0.6324	Remote Similarity	NPC235126
0.6324	Remote Similarity	NPC242419
0.6301	Remote Similarity	NPC277715
0.6267	Remote Similarity	NPC24960
0.5775	Remote Similarity	NPC177818
0.5732	Remote Similarity	NPC473616
0.5679	Remote Similarity	NPC131693
0.5679	Remote Similarity	NPC485591
0.5679	Remote Similarity	NPC475436
0.5556	Remote Similarity	NPC297348
0.5556	Remote Similarity	NPC325828
0.5556	Remote Similarity	NPC249204
0.5556	Remote Similarity	NPC48339
0.5556	Remote Similarity	NPC177834
0.5556	Remote Similarity	NPC141769
0.5556	Remote Similarity	NPC477547
0.5542	Remote Similarity	NPC312678
0.5542	Remote Similarity	NPC253268
0.5488	Remote Similarity	NPC234352
0.5479	Remote Similarity	NPC486119
0.5422	Remote Similarity	NPC477451
0.5362	Remote Similarity	NPC155985
0.5362	Remote Similarity	NPC601115
0.5357	Remote Similarity	NPC250393
0.5316	Remote Similarity	NPC481420
0.5316	Remote Similarity	NPC481421
0.5301	Remote Similarity	NPC294686
0.5294	Remote Similarity	NPC206003
0.5294	Remote Similarity	NPC473610
0.5244	Remote Similarity	NPC481424
0.5244	Remote Similarity	NPC481422
0.5244	Remote Similarity	NPC481423
0.5233	Remote Similarity	NPC211354
0.5233	Remote Similarity	NPC107188
0.5233	Remote Similarity	NPC19400
0.5211	Remote Similarity	NPC187159
0.5176	Remote Similarity	NPC222731
0.5172	Remote Similarity	NPC264101
0.5114	Remote Similarity	NPC107962
0.5067	Remote Similarity	NPC100451
0.506	Remote Similarity	NPC181845
0.5056	Remote Similarity	NPC6295

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC608477 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7317
0.1-0.2	1743
0.2-0.3	66
0.3-0.4	13
0.4-0.5	6
0.5-0.6	2
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	NPD6928	Phase 2
0.5584	Remote Similarity	NPD7991	Discontinued
0.5556	Remote Similarity	NPD8171	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