NPASS Compound

Natural Product: NPC601559

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 93 97 0 0 0 0 0 0 0 0999 V2000 6.6596 -2.9942 -1.8940 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7573 -2.6814 -0.4328 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8484 -1.7000 -0.1062 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6591 -0.3755 -0.7910 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3609 0.2898 -0.3953 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2190 1.6294 -1.1091 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9344 2.2895 -0.7145 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1065 1.7031 0.1365 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8581 2.3715 0.5061 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6507 1.5906 0.1583 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4178 1.1566 -0.9974 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7486 1.3253 1.1344 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4613 0.6111 1.0437 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4279 1.2622 0.1099 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8831 2.5201 0.6505 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5643 3.7437 0.0589 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8416 3.6623 -0.9941 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0060 5.0104 0.5827 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7875 5.0619 1.7130 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2024 6.3069 2.2175 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8348 7.4731 1.5932 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0528 7.4158 0.4620 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6535 6.1844 -0.0215 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6218 0.4827 -0.2831 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0570 1.0213 -1.6570 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4416 -0.9883 -0.4431 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7804 -1.1407 -1.6981 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5255 -1.6438 0.5520 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9589 -2.8580 -0.1525 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5016 -3.7083 -1.0007 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6700 -4.8241 -1.5313 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2326 -6.0554 -1.1914 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9045 -3.7168 -1.5355 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7604 -3.1387 -0.4888 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5595 -3.6700 0.7546 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2482 -3.2873 -0.7146 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8881 -4.0389 -1.4465 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7473 -2.2430 0.2198 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0621 -2.3123 0.9422 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8473 -1.2726 0.2886 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7477 -1.6374 -0.5855 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4703 -0.8212 1.1480 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8546 -0.0229 2.3371 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1398 -0.0369 3.4918 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2617 0.1821 2.7776 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7243 -4.0955 -2.0410 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4768 -2.4964 -2.4650 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6919 -2.6589 -2.2947 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9484 -3.6077 0.1488 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7968 -2.2489 -0.0795 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8558 -2.0844 -0.3206 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7658 -1.4884 1.0015 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7059 -0.5398 -1.8819 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5326 0.2801 -0.5294 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5297 -0.3345 -0.7401 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3643 0.4549 0.7053 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0534 2.2589 -0.7958 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2521 1.5097 -2.2017 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6882 3.2561 -1.1343 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3585 0.7399 0.5482 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8836 2.5192 1.6082 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8255 3.4009 0.0857 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8563 1.5285 -0.8022 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1158 4.1964 2.2558 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8149 6.3745 3.1003 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1709 8.4427 2.0061 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7768 8.3438 -0.0103 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0284 6.1556 -0.9282 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4589 0.7562 0.3928 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2879 0.2332 -2.3732 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9062 1.7055 -1.5939 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2271 1.6125 -2.1370 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1680 -0.4042 -1.8771 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0804 -2.0843 1.4342 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0814 -3.0765 0.0745 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6322 -4.7288 -2.6446 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3584 -4.8204 -1.1219 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8982 -6.3596 -1.8631 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2279 -4.7845 -1.7025 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0057 -3.1915 -2.4828 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2778 -3.4791 1.3788 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6185 -1.3525 0.8263 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6512 -3.1453 0.5650 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8532 -2.4394 2.0243 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0301 -0.4071 0.9324 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1221 -1.4295 -1.6395 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5432 -1.3237 1.1850 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3964 1.0061 3.7683 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0814 -0.5445 3.1868 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2921 -0.6229 4.3165 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5315 1.2566 2.5538 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9998 -0.5320 2.3871 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3866 0.1231 3.9006 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 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 10 11 2 0 10 12 1 0 13 12 1 1 13 14 1 0 14 15 1 0 15 16 1 0 16 17 2 0 16 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 14 24 1 0 24 25 1 0 24 26 1 0 26 27 1 6 26 28 1 0 28 29 1 0 29 30 2 0 30 31 1 0 31 32 1 0 30 33 1 0 33 34 1 0 34 35 1 1 34 36 1 0 36 37 2 0 36 38 1 0 38 39 1 0 38 40 2 0 40 41 1 0 28 42 1 0 42 43 1 0 43 44 1 0 43 45 1 0 42 13 1 0 43 13 1 0 23 18 1 0 41 26 1 0 41 34 1 0 1 46 1 0 1 47 1 0 1 48 1 0 2 49 1 0 2 50 1 0 3 51 1 0 3 52 1 0 4 53 1 0 4 54 1 0 5 55 1 0 5 56 1 0 6 57 1 0 6 58 1 0 7 59 1 0 8 60 1 0 9 61 1 0 9 62 1 0 14 63 1 6 19 64 1 0 20 65 1 0 21 66 1 0 22 67 1 0 23 68 1 0 24 69 1 1 25 70 1 0 25 71 1 0 25 72 1 0 27 73 1 0 28 74 1 1 29 75 1 0 31 76 1 0 31 77 1 0 32 78 1 0 33 79 1 0 33 80 1 0 35 81 1 0 39 82 1 0 39 83 1 0 39 84 1 0 40 85 1 0 41 86 1 6 42 87 1 1 44 88 1 0 44 89 1 0 44 90 1 0 45 91 1 0 45 92 1 0 45 93 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 NPC601559 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	7685
0.1-0.2	39636
0.2-0.3	2197
0.3-0.4	233
0.4-0.5	56
0.5-0.6	22
0.6-0.7	18
0.7-0.8	0
0.8-0.85	4
0.85-0.9	0
0.9-0.95	2
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9114	High Similarity	NPC283875
0.9103	High Similarity	NPC601392
0.8481	Intermediate Similarity	NPC138641
0.8481	Intermediate Similarity	NPC611243
0.8	Intermediate Similarity	NPC472398
0.8	Intermediate Similarity	NPC600915
0.7976	Intermediate Similarity	NPC22571
0.7976	Intermediate Similarity	NPC600480
0.7356	Intermediate Similarity	NPC603807
0.6705	Remote Similarity	NPC11410
0.6705	Remote Similarity	NPC600144
0.6667	Remote Similarity	NPC484333
0.6556	Remote Similarity	NPC601964
0.6477	Remote Similarity	NPC469647
0.6477	Remote Similarity	NPC469648
0.6265	Remote Similarity	NPC275696
0.6265	Remote Similarity	NPC255081
0.619	Remote Similarity	NPC5991
0.619	Remote Similarity	NPC196500
0.619	Remote Similarity	NPC471108
0.619	Remote Similarity	NPC5989
0.6163	Remote Similarity	NPC22628
0.6154	Remote Similarity	NPC482198
0.6111	Remote Similarity	NPC482199
0.6111	Remote Similarity	NPC482197
0.6087	Remote Similarity	NPC486559
0.6044	Remote Similarity	NPC486562
0.5977	Remote Similarity	NPC600005
0.5976	Remote Similarity	NPC171905
0.5851	Remote Similarity	NPC145649
0.5851	Remote Similarity	NPC233581
0.5833	Remote Similarity	NPC472758
0.5783	Remote Similarity	NPC472397
0.5778	Remote Similarity	NPC481523
0.5765	Remote Similarity	NPC471125
0.5667	Remote Similarity	NPC145238
0.5647	Remote Similarity	NPC157252
0.5568	Remote Similarity	NPC471128
0.5568	Remote Similarity	NPC471126
0.5517	Remote Similarity	NPC145182
0.5417	Remote Similarity	NPC479001
0.5417	Remote Similarity	NPC479002
0.5393	Remote Similarity	NPC485732
0.5333	Remote Similarity	NPC243902
0.5275	Remote Similarity	NPC478999
0.5258	Remote Similarity	NPC486560
0.5227	Remote Similarity	NPC482454
0.5213	Remote Similarity	NPC153651
0.5109	Remote Similarity	NPC132652

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC601559 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3234
0.1-0.2	5789
0.2-0.3	127
0.3-0.4	0
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