NPASS Compound

Natural Product: NPC607428

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 84 88 0 0 0 0 0 0 0 0999 V2000 -2.6112 3.4872 -4.7376 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7226 3.4622 -3.5499 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0970 4.4723 -3.2096 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5926 2.3118 -2.8239 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7756 2.1501 -1.6665 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2006 1.0577 -2.0157 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1093 0.7457 -0.8290 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0399 1.8681 -0.5999 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2794 0.2470 0.2700 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1475 -1.0479 -0.1556 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2615 -1.9729 0.7503 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6346 -2.5362 0.5819 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6569 -3.1953 0.8256 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1585 -1.1958 2.0495 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1994 -0.7405 2.3838 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9132 0.0282 1.3026 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5755 -0.8483 0.4346 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9650 -0.9403 0.3774 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5810 -0.1679 1.1824 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6875 -1.8353 -0.5146 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0969 -2.6604 -1.4340 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8341 -3.5034 -2.2423 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2047 -3.5422 -2.1490 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8237 -2.7281 -1.2387 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0577 -1.8774 -0.4251 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0007 0.9913 0.5763 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7671 2.1686 1.5193 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6903 1.5719 -0.6019 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5989 2.5468 -0.1400 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9165 2.6613 -0.3865 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7384 3.7496 0.2027 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4758 1.8405 -1.1262 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9524 0.0541 1.5848 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3098 -0.1794 1.5931 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1380 0.3973 2.5549 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5635 1.1339 3.4077 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5738 0.1697 2.5840 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1072 -0.5874 1.6586 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5229 -0.8570 1.6276 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3833 -0.3937 2.5723 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7684 -0.6506 2.5274 C 0 0 0 0 0 0 0 0 0 0 0 0 9.2300 -1.4135 1.4558 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3751 -1.8891 0.4931 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0348 -1.6088 0.5863 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7449 2.4237 -5.0867 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6001 3.8735 -4.4038 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1506 4.1300 -5.5234 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2285 3.0364 -1.3844 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3727 0.1381 -2.2505 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8412 1.2998 -2.8872 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7208 -0.1271 -1.2235 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2349 2.1120 0.4377 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0503 1.5757 -1.0169 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8011 2.7837 -1.2197 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5366 -3.4633 -0.0653 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3798 -1.9323 0.0921 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9712 -2.9357 1.5679 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0608 -4.1582 0.7800 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3381 -3.2471 -0.0118 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1244 -3.2270 1.8243 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6353 -1.6606 2.9032 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8319 -1.5843 2.7025 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1177 -0.0661 3.2906 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6876 0.6205 1.8313 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0234 -2.6435 -1.5294 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3663 -4.1578 -2.9767 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7744 -4.2196 -2.7997 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8922 -2.7498 -1.1541 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5614 -1.2423 0.2812 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4677 3.0178 1.3189 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0267 1.8477 2.5508 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2243 2.5855 1.5138 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2718 0.8049 -1.1392 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9636 4.4623 -0.6323 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7089 3.3820 0.5984 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1536 4.3061 0.9613 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6808 0.7825 2.3854 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1556 0.6148 3.3473 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4303 -1.0108 0.8908 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0702 0.1989 3.4144 H 0 0 0 0 0 0 0 0 0 0 0 0 9.4014 -0.2638 3.2959 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3029 -1.5924 1.4484 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7735 -2.4811 -0.3348 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3436 -1.9767 -0.1600 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 7 9 1 0 9 10 1 6 10 11 1 0 11 12 1 0 11 13 1 0 11 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 18 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 24 25 2 0 16 26 1 0 26 27 1 1 26 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 30 32 2 0 14 33 1 0 33 34 1 0 34 35 1 0 35 36 2 0 35 37 1 0 37 38 2 0 38 39 1 0 39 40 2 0 40 41 1 0 41 42 2 0 42 43 1 0 43 44 2 0 28 5 1 0 44 39 1 0 26 9 1 0 33 9 1 0 25 20 1 0 1 45 1 0 1 46 1 0 1 47 1 0 5 48 1 1 6 49 1 0 6 50 1 0 7 51 1 6 8 52 1 0 8 53 1 0 8 54 1 0 12 55 1 0 12 56 1 0 12 57 1 0 13 58 1 0 13 59 1 0 13 60 1 0 14 61 1 1 15 62 1 0 15 63 1 0 16 64 1 1 21 65 1 0 22 66 1 0 23 67 1 0 24 68 1 0 25 69 1 0 27 70 1 0 27 71 1 0 27 72 1 0 28 73 1 6 31 74 1 0 31 75 1 0 31 76 1 0 33 77 1 1 37 78 1 0 38 79 1 0 40 80 1 0 41 81 1 0 42 82 1 0 43 83 1 0 44 84 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 NPC607428 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	15083
0.1-0.2	32089
0.2-0.3	2093
0.3-0.4	426
0.4-0.5	103
0.5-0.6	30
0.6-0.7	13
0.7-0.8	0
0.8-0.85	2
0.85-0.9	1
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9394	High Similarity	NPC473112
0.8551	High Similarity	NPC473085
0.806	Intermediate Similarity	NPC70973
0.8	Intermediate Similarity	NPC195647
0.7794	Intermediate Similarity	NPC473111
0.7727	Intermediate Similarity	NPC200592
0.7727	Intermediate Similarity	NPC610542
0.7639	Intermediate Similarity	NPC210591
0.7463	Intermediate Similarity	NPC473081
0.7432	Intermediate Similarity	NPC609221
0.7297	Intermediate Similarity	NPC473613
0.7206	Intermediate Similarity	NPC270498
0.7143	Intermediate Similarity	NPC605086
0.6974	Remote Similarity	NPC481050
0.6625	Remote Similarity	NPC483865
0.6447	Remote Similarity	NPC472574
0.64	Remote Similarity	NPC43241
0.6375	Remote Similarity	NPC14499
0.6316	Remote Similarity	NPC473673
0.6267	Remote Similarity	NPC479047
0.6267	Remote Similarity	NPC291638
0.6184	Remote Similarity	NPC177340
0.6076	Remote Similarity	NPC214550
0.6026	Remote Similarity	NPC479044
0.6	Remote Similarity	NPC311175
0.6	Remote Similarity	NPC475652
0.5976	Remote Similarity	NPC88593
0.5974	Remote Similarity	NPC139067
0.5952	Remote Similarity	NPC488916
0.589	Remote Similarity	NPC474608
0.5844	Remote Similarity	NPC4341
0.5769	Remote Similarity	NPC67777
0.5765	Remote Similarity	NPC188865
0.5765	Remote Similarity	NPC184817
0.5733	Remote Similarity	NPC481047
0.5733	Remote Similarity	NPC481045
0.5679	Remote Similarity	NPC184747
0.5676	Remote Similarity	NPC283375
0.5641	Remote Similarity	NPC483883
0.5641	Remote Similarity	NPC151585
0.5641	Remote Similarity	NPC191082
0.5595	Remote Similarity	NPC483878
0.5595	Remote Similarity	NPC603877
0.5584	Remote Similarity	NPC37641
0.5467	Remote Similarity	NPC183122
0.5412	Remote Similarity	NPC472571
0.5385	Remote Similarity	NPC114927
0.5366	Remote Similarity	NPC609924
0.5349	Remote Similarity	NPC473109
0.5263	Remote Similarity	NPC481066
0.5125	Remote Similarity	NPC163087
0.5114	Remote Similarity	NPC125106
0.5114	Remote Similarity	NPC472573
0.5062	Remote Similarity	NPC48017
0.5052	Remote Similarity	NPC483880
0.5052	Remote Similarity	NPC156941

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC607428 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4556
0.1-0.2	4495
0.2-0.3	98
0.3-0.4	1
0.4-0.5	0
0.5-0.6	0
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	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

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