NPASS Compound

Natural Product: NPC601567

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 103108 0 0 0 0 0 0 0 0999 V2000 5.9659 -2.7911 -3.9371 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2616 -2.7669 -3.4293 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6506 -2.2462 -2.2017 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8008 -1.6777 -1.3099 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2624 -1.1745 -0.0922 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2448 -0.5817 0.7852 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4995 -0.0614 1.9738 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3743 0.4933 2.7302 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4559 1.0084 3.8459 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0909 0.5177 2.3084 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9512 0.9857 2.8695 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5161 2.2285 2.1143 C 0 0 2 0 0 0 0 0 0 0 0 0 2.3974 3.3531 2.9702 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2071 2.1125 1.4021 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9096 0.6926 0.9118 C 0 0 2 0 0 0 0 0 0 0 0 0 2.0317 0.3610 -0.0113 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3670 0.6530 0.1502 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2098 1.8393 0.5449 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4301 1.8970 -0.3005 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0897 0.7734 -0.5545 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3059 0.9532 -1.4192 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0850 2.0500 -0.7754 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5555 2.0360 -0.9034 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2583 1.6859 0.4080 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0738 3.4500 -1.2325 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0112 1.1832 -2.0335 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4994 -0.2086 -1.8669 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9951 -0.2822 -1.7984 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.5424 -0.7190 -3.1489 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6888 -0.0374 -3.7631 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0133 -1.8553 -3.7862 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7004 -1.4867 -0.8965 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2035 -1.6718 -0.7476 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6027 -0.4771 0.0160 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.2451 -0.6158 1.4048 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1053 -0.6321 0.0886 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6854 -1.4078 -1.1901 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8171 -1.6262 1.1679 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5831 -1.5595 1.7504 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8141 -0.1320 2.1637 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8117 0.1044 3.2258 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1003 0.8016 4.4019 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3785 -1.1573 3.8567 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5779 -1.2407 0.2328 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4557 -1.8232 -0.6790 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0085 -2.3192 -1.8761 C 0 0 0 0 0 0 0 0 0 0 0 0 9.8944 -2.9018 -2.7863 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0260 -2.6415 -5.0390 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3423 -1.9652 -3.5235 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5110 -3.7837 -3.7842 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7444 -1.6239 -1.5677 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1988 -0.5532 0.4617 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5005 -0.0678 2.3292 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3308 1.3897 3.8623 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3361 2.5610 1.4062 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7660 4.0023 2.6267 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4035 2.5186 2.0215 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3502 2.6892 0.4352 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5504 -0.5770 0.2539 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8515 1.1417 -0.0402 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6946 0.3900 -1.0918 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0939 0.8883 -0.9326 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6197 2.7573 0.2883 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4996 1.9026 1.5827 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7487 2.8668 -0.6874 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8731 1.4090 -2.3657 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8637 2.1092 0.3360 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7145 3.0605 -1.1299 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4673 0.6273 0.5273 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2192 2.2429 0.5180 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6397 2.0023 1.2791 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6244 4.1901 -0.5463 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8862 3.6838 -2.2971 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1610 3.4576 -1.0725 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1341 1.1198 -1.9865 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6758 1.6575 -2.9785 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9845 -0.6560 -0.9754 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9082 -0.8054 -2.7343 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9569 -2.0308 -4.7813 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0537 -2.3681 -1.4823 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2615 -1.4819 0.0324 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0764 -2.5746 -0.1213 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8309 -1.7392 -1.7715 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4187 -1.6731 1.6745 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3058 -0.2171 1.2941 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8046 0.0215 2.1617 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0901 -2.4587 -1.0764 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0024 -0.9074 -2.0982 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4176 -1.6010 -1.1771 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4622 -1.4253 2.0742 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9628 -2.6632 0.8074 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5257 -2.2665 2.6059 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3412 -1.9745 1.0663 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2017 0.1687 2.5559 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0081 0.6588 4.3283 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4018 0.4342 5.3773 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2629 1.8906 4.3848 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9673 -0.8502 4.7582 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9018 -1.8073 3.1685 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5686 -1.7991 4.2883 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9321 -0.8576 1.1597 H 0 0 0 0 0 0 0 0 0 0 0 0 10.4996 -1.8718 -0.4131 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3652 -2.3272 -3.4944 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 12 14 1 0 14 15 1 0 15 16 1 6 15 17 1 0 17 18 1 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 23 25 1 0 23 26 1 0 26 27 1 0 27 28 1 0 28 29 1 6 29 30 2 0 29 31 1 0 28 32 1 0 32 33 1 0 33 34 1 0 34 35 1 1 34 36 1 0 36 37 1 6 36 38 1 0 38 39 1 0 39 40 1 0 40 41 1 0 41 42 1 0 41 43 1 0 5 44 2 0 44 45 1 0 45 46 2 0 46 47 1 0 46 3 1 0 41 11 1 0 40 15 1 0 36 17 1 0 34 20 1 0 28 21 1 0 1 48 1 0 1 49 1 0 1 50 1 0 4 51 1 0 6 52 1 0 7 53 1 0 11 54 1 1 12 55 1 6 13 56 1 0 14 57 1 0 14 58 1 0 16 59 1 0 16 60 1 0 16 61 1 0 17 62 1 0 18 63 1 0 18 64 1 0 19 65 1 0 21 66 1 0 22 67 1 0 22 68 1 0 24 69 1 0 24 70 1 0 24 71 1 0 25 72 1 0 25 73 1 0 25 74 1 0 26 75 1 0 26 76 1 0 27 77 1 0 27 78 1 0 31 79 1 0 32 80 1 0 32 81 1 0 33 82 1 0 33 83 1 0 35 84 1 0 35 85 1 0 35 86 1 0 37 87 1 0 37 88 1 0 37 89 1 0 38 90 1 0 38 91 1 0 39 92 1 0 39 93 1 0 40 94 1 1 42 95 1 0 42 96 1 0 42 97 1 0 43 98 1 0 43 99 1 0 43100 1 0 44101 1 0 45102 1 0 47103 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 NPC601567 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	5790
0.1-0.2	38424
0.2-0.3	4887
0.3-0.4	509
0.4-0.5	173
0.5-0.6	43
0.6-0.7	13
0.7-0.8	0
0.8-0.85	6
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC606631
0.8571	High Similarity	NPC605663
0.8298	Intermediate Similarity	NPC610795
0.8247	Intermediate Similarity	NPC481234
0.8247	Intermediate Similarity	NPC118033
0.8247	Intermediate Similarity	NPC479431
0.8043	Intermediate Similarity	NPC171007
0.8043	Intermediate Similarity	NPC190849
0.7	Intermediate Similarity	NPC304110
0.7	Intermediate Similarity	NPC25491
0.7	Intermediate Similarity	NPC27518
0.7	Intermediate Similarity	NPC611516
0.6869	Remote Similarity	NPC22676
0.6863	Remote Similarity	NPC482051
0.6667	Remote Similarity	NPC206232
0.6667	Remote Similarity	NPC14515
0.6574	Remote Similarity	NPC481235
0.6505	Remote Similarity	NPC132126
0.6442	Remote Similarity	NPC178093
0.6381	Remote Similarity	NPC324798
0.6381	Remote Similarity	NPC479742
0.6321	Remote Similarity	NPC479745
0.6311	Remote Similarity	NPC198621
0.6311	Remote Similarity	NPC216940
0.6075	Remote Similarity	NPC475311
0.5702	Remote Similarity	NPC53520
0.5701	Remote Similarity	NPC470618
0.5701	Remote Similarity	NPC470619
0.5648	Remote Similarity	NPC172311
0.5648	Remote Similarity	NPC488214
0.5648	Remote Similarity	NPC482052
0.5607	Remote Similarity	NPC101863
0.5575	Remote Similarity	NPC310729
0.5575	Remote Similarity	NPC150310
0.5556	Remote Similarity	NPC262970
0.5524	Remote Similarity	NPC43353
0.5463	Remote Similarity	NPC488215
0.5455	Remote Similarity	NPC205392
0.5455	Remote Similarity	NPC233012
0.5455	Remote Similarity	NPC105942
0.5405	Remote Similarity	NPC479739
0.5398	Remote Similarity	NPC473680
0.5368	Remote Similarity	NPC120840
0.5364	Remote Similarity	NPC479744
0.5354	Remote Similarity	NPC230151
0.5278	Remote Similarity	NPC477874
0.5268	Remote Similarity	NPC485425
0.5263	Remote Similarity	NPC479740
0.5263	Remote Similarity	NPC479741
0.5234	Remote Similarity	NPC173569
0.5185	Remote Similarity	NPC475138
0.5182	Remote Similarity	NPC477873
0.5179	Remote Similarity	NPC606782
0.514	Remote Similarity	NPC485587
0.5133	Remote Similarity	NPC479747
0.5133	Remote Similarity	NPC479746
0.5133	Remote Similarity	NPC482049
0.5133	Remote Similarity	NPC482050
0.5104	Remote Similarity	NPC231063
0.5104	Remote Similarity	NPC282395
0.5104	Remote Similarity	NPC481360
0.5104	Remote Similarity	NPC110308
0.5088	Remote Similarity	NPC473773
0.5088	Remote Similarity	NPC475579
0.5052	Remote Similarity	NPC200752
0.5051	Remote Similarity	NPC296164
0.5043	Remote Similarity	NPC475454
0.5043	Remote Similarity	NPC473579

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC601567 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	2989
0.1-0.2	6042
0.2-0.3	117
0.3-0.4	1
0.4-0.5	0
0.5-0.6	1
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
0.5179	Remote Similarity	NPD8166	Discontinued

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