NPASS Compound

Natural Product: NPC607401

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 85 91 0 0 0 0 0 0 0 0999 V2000 0.5329 -2.7823 3.2700 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5910 -1.8521 2.2093 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5183 -1.6841 1.4091 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6731 -2.4312 1.6586 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7668 -2.2714 0.8761 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7348 -1.3620 -0.1722 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5988 -0.6326 -0.4126 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4582 -0.7609 0.3568 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6882 -0.0732 0.1726 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7765 -0.2587 -0.6115 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7230 -1.1408 -1.6599 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5435 -1.8679 -1.9365 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3638 -3.1930 -1.4266 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7957 -1.3887 -2.5152 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6796 -2.2975 -3.5616 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7350 -2.5802 -4.4456 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9499 -0.7017 -2.2719 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0311 0.1783 -1.2401 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9375 0.4241 -0.3766 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2307 1.4076 0.6592 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2643 1.7139 1.7113 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5637 3.0286 1.4653 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2740 4.2166 1.5608 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7049 5.4484 1.3527 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3640 5.5153 1.0331 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2509 6.7400 0.8146 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3677 4.3297 0.9322 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2345 3.1133 1.1475 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7080 4.4219 0.6109 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4707 3.3138 0.3602 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7652 2.4289 1.3674 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5432 1.2977 1.1160 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0110 1.0804 -0.1505 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7276 1.9493 -1.1629 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9509 3.0758 -0.9061 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8451 -0.1060 -0.4218 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9553 -1.2178 -0.9604 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.6937 -2.3970 -1.1946 N 0 0 0 0 0 0 0 0 0 0 0 0 -6.1139 -2.1458 -1.4269 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4606 -3.4790 -0.3323 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0194 -3.0759 1.0835 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5111 1.0383 1.2609 N 0 0 0 0 0 0 0 0 0 0 0 0 4.5065 -0.2869 1.8115 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6057 1.2845 0.3652 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3147 0.8909 -1.0489 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4859 -3.8300 2.9002 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4606 -2.7420 3.8995 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3375 -2.5964 3.9278 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6680 -3.1306 2.4817 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5327 0.0807 -1.2200 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7113 -3.2970 -1.1480 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9549 -3.3471 -0.4986 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5828 -3.9653 -2.2055 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9198 -1.7700 -5.1896 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5202 -3.5083 -5.0118 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6961 -2.7646 -3.8994 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7967 -0.9018 -2.9528 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4724 2.3946 0.1344 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7643 1.8615 2.7216 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5235 0.9413 1.8664 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3248 4.1385 1.8135 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3008 6.3765 1.4376 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3333 7.1713 -0.0915 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3492 2.2228 1.0688 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4091 2.5755 2.3769 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7732 0.6014 1.9073 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0798 1.8060 -2.1652 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7093 3.7812 -1.6836 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2985 -0.4490 0.5319 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6897 0.0980 -1.1052 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6267 -0.8332 -1.9740 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5862 -1.6383 -0.5690 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6691 -3.0777 -1.6038 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1913 -1.5328 -2.3457 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5984 -4.0756 -0.7351 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3745 -4.1322 -0.2611 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8246 -4.0223 1.6197 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7943 -2.5273 1.6164 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8939 -0.3635 2.7390 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2433 -1.0770 1.0961 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5576 -0.4953 2.1369 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8945 2.3518 0.4452 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4772 0.7013 0.7179 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2794 1.8091 -1.6699 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1194 0.2555 -1.4792 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 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 1 0 11 14 1 0 14 15 1 0 15 16 1 0 14 17 2 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 2 0 23 24 1 0 24 25 2 0 25 26 1 0 25 27 1 0 27 28 2 0 27 29 1 0 29 30 1 0 30 31 2 0 31 32 1 0 32 33 2 0 33 34 1 0 34 35 2 0 33 36 1 0 36 37 1 0 37 38 1 0 38 39 1 0 38 40 1 0 40 41 1 0 20 42 1 0 42 43 1 0 42 44 1 0 44 45 1 0 8 3 1 0 19 10 1 0 28 22 1 0 35 30 1 0 41 5 1 0 37 6 1 0 45 18 1 0 1 46 1 0 1 47 1 0 1 48 1 0 4 49 1 0 7 50 1 0 13 51 1 0 13 52 1 0 13 53 1 0 16 54 1 0 16 55 1 0 16 56 1 0 17 57 1 0 20 58 1 6 21 59 1 0 21 60 1 0 23 61 1 0 24 62 1 0 26 63 1 0 28 64 1 0 31 65 1 0 32 66 1 0 34 67 1 0 35 68 1 0 36 69 1 0 36 70 1 0 37 71 1 6 39 72 1 0 39 73 1 0 39 74 1 0 40 75 1 0 40 76 1 0 41 77 1 0 41 78 1 0 43 79 1 0 43 80 1 0 43 81 1 0 44 82 1 0 44 83 1 0 45 84 1 0 45 85 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 NPC607401 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	28960
0.1-0.2	19252
0.2-0.3	1375
0.3-0.4	131
0.4-0.5	27
0.5-0.6	36
0.6-0.7	22
0.7-0.8	1
0.8-0.85	17
0.85-0.9	1
0.9-0.95	2
0.95-1	4

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC185639
1.0	High Similarity	NPC251735
1.0	High Similarity	NPC49075
1.0	High Similarity	NPC599951
0.9429	High Similarity	NPC223690
0.9429	High Similarity	NPC9532
0.88	High Similarity	NPC24260
0.8421	Intermediate Similarity	NPC212237
0.8312	Intermediate Similarity	NPC611658
0.8267	Intermediate Similarity	NPC274716
0.8267	Intermediate Similarity	NPC167116
0.8267	Intermediate Similarity	NPC609821
0.8158	Intermediate Similarity	NPC181796
0.8158	Intermediate Similarity	NPC54654
0.8158	Intermediate Similarity	NPC7715
0.8158	Intermediate Similarity	NPC328155
0.8158	Intermediate Similarity	NPC222661
0.8158	Intermediate Similarity	NPC285931
0.8028	Intermediate Similarity	NPC76682
0.8028	Intermediate Similarity	NPC10908
0.8028	Intermediate Similarity	NPC63646
0.8028	Intermediate Similarity	NPC317145
0.8028	Intermediate Similarity	NPC198498
0.8028	Intermediate Similarity	NPC115284
0.7922	Intermediate Similarity	NPC290005
0.7714	Intermediate Similarity	NPC317272
0.7714	Intermediate Similarity	NPC268503
0.7671	Intermediate Similarity	NPC276890
0.7561	Intermediate Similarity	NPC480590
0.7403	Intermediate Similarity	NPC608819
0.7397	Intermediate Similarity	NPC256012
0.7397	Intermediate Similarity	NPC610965
0.7308	Intermediate Similarity	NPC311973
0.7273	Intermediate Similarity	NPC480587
0.7262	Intermediate Similarity	NPC206900
0.7209	Intermediate Similarity	NPC41122
0.7209	Intermediate Similarity	NPC318805
0.7195	Intermediate Similarity	NPC8836
0.716	Intermediate Similarity	NPC16357
0.716	Intermediate Similarity	NPC302245
0.7143	Intermediate Similarity	NPC480586
0.7089	Intermediate Similarity	NPC239824
0.7051	Intermediate Similarity	NPC290582
0.7051	Intermediate Similarity	NPC217748
0.7051	Intermediate Similarity	NPC73492
0.7051	Intermediate Similarity	NPC182052
0.7051	Intermediate Similarity	NPC271013
0.7051	Intermediate Similarity	NPC299990
0.7051	Intermediate Similarity	NPC42663
0.7051	Intermediate Similarity	NPC15414
0.7013	Intermediate Similarity	NPC240841
0.7	Intermediate Similarity	NPC254441
0.7	Intermediate Similarity	NPC116465
0.6962	Remote Similarity	NPC279228
0.6812	Remote Similarity	NPC317439
0.6795	Remote Similarity	NPC12424
0.6795	Remote Similarity	NPC129518
0.6795	Remote Similarity	NPC251580
0.6709	Remote Similarity	NPC603853
0.6667	Remote Similarity	NPC227060
0.6582	Remote Similarity	NPC610959
0.641	Remote Similarity	NPC480592
0.631	Remote Similarity	NPC229373
0.6301	Remote Similarity	NPC247639
0.6301	Remote Similarity	NPC25084
0.6296	Remote Similarity	NPC480591
0.625	Remote Similarity	NPC603603
0.6196	Remote Similarity	NPC60295
0.6196	Remote Similarity	NPC191132
0.619	Remote Similarity	NPC601503
0.6146	Remote Similarity	NPC475654
0.6129	Remote Similarity	NPC175890
0.6087	Remote Similarity	NPC85381
0.6071	Remote Similarity	NPC600054
0.6071	Remote Similarity	NPC601504
0.5957	Remote Similarity	NPC201508
0.5909	Remote Similarity	NPC139783
0.5909	Remote Similarity	NPC65312
0.5909	Remote Similarity	NPC475479
0.5909	Remote Similarity	NPC323537
0.5909	Remote Similarity	NPC611798
0.5843	Remote Similarity	NPC485712
0.5843	Remote Similarity	NPC275680
0.5843	Remote Similarity	NPC22115
0.5795	Remote Similarity	NPC195538
0.5732	Remote Similarity	NPC41376
0.573	Remote Similarity	NPC243454
0.573	Remote Similarity	NPC601489
0.573	Remote Similarity	NPC604804
0.5714	Remote Similarity	NPC10871
0.5667	Remote Similarity	NPC605743
0.5658	Remote Similarity	NPC104196
0.5517	Remote Similarity	NPC286119
0.5479	Remote Similarity	NPC185838
0.5432	Remote Similarity	NPC30779
0.5263	Remote Similarity	NPC11296
0.5263	Remote Similarity	NPC281581
0.5263	Remote Similarity	NPC254581
0.5263	Remote Similarity	NPC135538
0.5263	Remote Similarity	NPC274661
0.5263	Remote Similarity	NPC24233
0.5263	Remote Similarity	NPC82457
0.5208	Remote Similarity	NPC485711
0.5169	Remote Similarity	NPC600872
0.5139	Remote Similarity	NPC314682
0.5102	Remote Similarity	NPC475597
0.5068	Remote Similarity	NPC213206
0.5068	Remote Similarity	NPC188163
0.5068	Remote Similarity	NPC328750
0.5053	Remote Similarity	NPC239584
0.5051	Remote Similarity	NPC234318

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC607401 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4732
0.1-0.2	4308
0.2-0.3	99
0.3-0.4	5
0.4-0.5	0
0.5-0.6	2
0.6-0.7	2
0.7-0.8	1
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8028	Intermediate Similarity	NPD8099	Discontinued
0.7368	Intermediate Similarity	NPD8156	Discontinued
0.6625	Remote Similarity	NPD8095	Phase 1
0.6196	Remote Similarity	NPD8053	Approved
0.5957	Remote Similarity	NPD8054	Phase 4
0.5068	Remote Similarity	NPD4664	Clinical (unspecified phase)

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