NPASS Compound

Natural Product: NPC607851

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 82 86 0 0 0 0 0 0 0 0999 V2000 -2.6219 2.4417 -0.7045 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5471 1.3183 -0.3417 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.8642 1.6273 -1.0743 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.5230 2.8310 -0.4337 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7040 0.3736 -0.9249 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2543 -0.4658 0.2514 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8911 -1.0693 0.0580 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.9117 -2.3139 -0.7136 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2757 -2.4003 -1.7937 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6101 -3.4541 -0.3262 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2334 -1.1809 1.3829 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7860 -1.6491 1.3319 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9151 -0.6384 0.6127 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8207 0.4966 1.5765 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6321 -0.3045 -0.6520 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9801 -0.2578 -1.7988 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4584 -0.5059 -2.0336 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1208 -0.3108 -0.7168 C 0 0 2 0 0 0 0 0 0 0 0 0 2.6097 -0.2725 -0.7624 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2786 -1.5354 -1.1663 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0054 0.7215 -1.8714 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3422 1.3031 -1.7445 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1703 1.0679 -0.5585 C 0 0 2 0 0 0 0 0 0 0 0 0 6.3227 0.2858 -0.8554 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5506 0.4816 0.6537 C 0 0 1 0 0 0 0 0 0 0 0 0 5.2282 -0.7859 1.0811 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7397 1.4579 1.8345 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1386 2.6824 1.5636 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0661 0.3700 0.4972 C 0 0 2 0 0 0 0 0 0 0 0 0 2.3359 -0.0934 1.7098 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3874 -1.2221 1.5022 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4827 -1.1574 0.3308 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2941 -2.6105 -0.1110 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0764 -0.0252 -0.7234 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.1534 3.3444 -1.0734 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0035 2.0799 -1.5725 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9783 2.7801 0.1272 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9154 1.3974 0.7253 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6804 1.7830 -2.1526 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6070 2.6800 -0.2619 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0782 3.0565 0.5704 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4008 3.7408 -1.0555 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7551 -0.2148 -1.8449 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7339 0.7160 -0.6901 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3901 0.0694 1.1902 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9758 -1.3347 0.2848 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8119 -4.1890 -1.0182 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3876 -0.2767 1.9629 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7729 -1.9995 1.9473 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8108 -2.6332 0.8413 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5531 -1.7017 2.4203 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5546 0.1054 2.5832 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8085 0.9895 1.7755 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1793 1.3319 1.2448 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5517 -0.0068 -2.6983 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6510 -1.4908 -2.5034 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8504 0.2304 -2.7978 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8338 0.7550 -0.4206 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5015 -2.2631 -0.3986 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2737 -1.3439 -1.6791 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6759 -1.9461 -2.0326 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2045 1.5126 -1.8256 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8794 0.1600 -2.8383 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2488 2.4136 -1.9710 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9572 0.9655 -2.6398 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6629 2.0560 -0.2874 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0158 0.4297 -0.1667 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0845 -0.5516 1.7827 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6189 -1.5249 1.5860 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7426 -1.3021 0.2167 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8421 1.6622 1.8728 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4718 1.0182 2.7903 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7368 3.3224 1.1116 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7552 1.4635 0.3901 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1191 -0.4598 2.4398 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8791 0.7504 2.3145 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0374 -2.1541 1.4788 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8510 -1.3575 2.4819 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1243 -3.2527 0.8009 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5571 -2.7587 -0.7597 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2416 -3.0579 -0.4823 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4846 -0.2001 -1.7674 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 3 5 1 0 5 6 1 0 6 7 1 0 7 8 1 6 8 9 2 0 8 10 1 0 7 11 1 0 11 12 1 0 12 13 1 0 13 14 1 1 13 15 1 0 15 16 2 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 6 19 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 23 25 1 0 25 26 1 1 25 27 1 0 27 28 1 0 25 29 1 0 29 30 1 0 30 31 1 0 31 32 1 0 32 33 1 6 15 34 1 0 34 2 1 0 34 7 1 0 32 13 1 0 32 18 1 0 29 19 1 0 1 35 1 0 1 36 1 0 1 37 1 0 2 38 1 1 3 39 1 6 4 40 1 0 4 41 1 0 4 42 1 0 5 43 1 0 5 44 1 0 6 45 1 0 6 46 1 0 10 47 1 0 11 48 1 0 11 49 1 0 12 50 1 0 12 51 1 0 14 52 1 0 14 53 1 0 14 54 1 0 16 55 1 0 17 56 1 0 17 57 1 0 18 58 1 1 20 59 1 0 20 60 1 0 20 61 1 0 21 62 1 0 21 63 1 0 22 64 1 0 22 65 1 0 23 66 1 1 24 67 1 0 26 68 1 0 26 69 1 0 26 70 1 0 27 71 1 0 27 72 1 0 28 73 1 0 29 74 1 6 30 75 1 0 30 76 1 0 31 77 1 0 31 78 1 0 33 79 1 0 33 80 1 0 33 81 1 0 34 82 1 6 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 NPC607851 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	24051
0.1-0.2	21505
0.2-0.3	3359
0.3-0.4	586
0.4-0.5	210
0.5-0.6	86
0.6-0.7	32
0.7-0.8	0
0.8-0.85	0
0.85-0.9	3
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC61543
1.0	High Similarity	NPC293048
1.0	High Similarity	NPC225585
0.8525	High Similarity	NPC51700
0.8525	High Similarity	NPC88716
0.8525	High Similarity	NPC68160
0.7727	Intermediate Similarity	NPC127689
0.7692	Intermediate Similarity	NPC32407
0.7692	Intermediate Similarity	NPC263548
0.7692	Intermediate Similarity	NPC606320
0.75	Intermediate Similarity	NPC274330
0.7385	Intermediate Similarity	NPC270768
0.7385	Intermediate Similarity	NPC59263
0.7385	Intermediate Similarity	NPC210106
0.7385	Intermediate Similarity	NPC229281
0.7385	Intermediate Similarity	NPC121798
0.7385	Intermediate Similarity	NPC234346
0.7313	Intermediate Similarity	NPC191412
0.7313	Intermediate Similarity	NPC114159
0.7313	Intermediate Similarity	NPC6818
0.7164	Intermediate Similarity	NPC173089
0.7015	Intermediate Similarity	NPC71074
0.7015	Intermediate Similarity	NPC605937
0.6957	Remote Similarity	NPC130520
0.6857	Remote Similarity	NPC116457
0.6818	Remote Similarity	NPC274050
0.6818	Remote Similarity	NPC162632
0.6667	Remote Similarity	NPC305464
0.6667	Remote Similarity	NPC87095
0.6667	Remote Similarity	NPC19376
0.6667	Remote Similarity	NPC25848
0.6667	Remote Similarity	NPC477288
0.6571	Remote Similarity	NPC263393
0.6571	Remote Similarity	NPC485589
0.6471	Remote Similarity	NPC477289
0.6429	Remote Similarity	NPC293564
0.6429	Remote Similarity	NPC136697
0.641	Remote Similarity	NPC57362
0.6377	Remote Similarity	NPC182797
0.6377	Remote Similarity	NPC52169
0.6377	Remote Similarity	NPC195019
0.6377	Remote Similarity	NPC488562
0.6351	Remote Similarity	NPC230151
0.6329	Remote Similarity	NPC177246
0.6232	Remote Similarity	NPC480946
0.6232	Remote Similarity	NPC187722
0.6232	Remote Similarity	NPC130577
0.6232	Remote Similarity	NPC142415
0.6232	Remote Similarity	NPC102683
0.6197	Remote Similarity	NPC202728
0.6197	Remote Similarity	NPC158059
0.6111	Remote Similarity	NPC610635
0.6056	Remote Similarity	NPC37221
0.6	Remote Similarity	NPC485586
0.6	Remote Similarity	NPC485588
0.5972	Remote Similarity	NPC40092
0.5972	Remote Similarity	NPC298554
0.5946	Remote Similarity	NPC187933
0.5946	Remote Similarity	NPC20235
0.5946	Remote Similarity	NPC299996
0.5915	Remote Similarity	NPC606443
0.5909	Remote Similarity	NPC475482
0.5833	Remote Similarity	NPC88116
0.5811	Remote Similarity	NPC137072
0.5811	Remote Similarity	NPC477290
0.5775	Remote Similarity	NPC198664
0.5733	Remote Similarity	NPC117663
0.5682	Remote Similarity	NPC479744
0.5676	Remote Similarity	NPC247139
0.5634	Remote Similarity	NPC242631
0.5625	Remote Similarity	NPC485585
0.5616	Remote Similarity	NPC231063
0.5616	Remote Similarity	NPC282395
0.5616	Remote Similarity	NPC73489
0.5616	Remote Similarity	NPC130278
0.5616	Remote Similarity	NPC173744
0.5616	Remote Similarity	NPC204961
0.5616	Remote Similarity	NPC73004
0.5616	Remote Similarity	NPC609452
0.5588	Remote Similarity	NPC196753
0.5479	Remote Similarity	NPC171203
0.5479	Remote Similarity	NPC307426
0.5479	Remote Similarity	NPC98442
0.5479	Remote Similarity	NPC242468
0.5479	Remote Similarity	NPC479079
0.5455	Remote Similarity	NPC479743
0.5429	Remote Similarity	NPC230295
0.5429	Remote Similarity	NPC98386
0.5422	Remote Similarity	NPC485882
0.5417	Remote Similarity	NPC477872
0.5405	Remote Similarity	NPC38754
0.5395	Remote Similarity	NPC25299
0.5395	Remote Similarity	NPC481322
0.5342	Remote Similarity	NPC213412
0.5341	Remote Similarity	NPC475457
0.5333	Remote Similarity	NPC479077
0.5278	Remote Similarity	NPC488164
0.5278	Remote Similarity	NPC264005
0.527	Remote Similarity	NPC7260
0.527	Remote Similarity	NPC210037
0.527	Remote Similarity	NPC282616
0.527	Remote Similarity	NPC275809
0.527	Remote Similarity	NPC120968
0.527	Remote Similarity	NPC227467
0.527	Remote Similarity	NPC273621
0.5263	Remote Similarity	NPC118519
0.5263	Remote Similarity	NPC132824
0.5233	Remote Similarity	NPC485587
0.5217	Remote Similarity	NPC479747
0.5217	Remote Similarity	NPC479746
0.5217	Remote Similarity	NPC178093
0.5211	Remote Similarity	NPC253402
0.52	Remote Similarity	NPC158141
0.52	Remote Similarity	NPC472149
0.52	Remote Similarity	NPC300351
0.52	Remote Similarity	NPC110308
0.5195	Remote Similarity	NPC148964
0.5172	Remote Similarity	NPC173569
0.5165	Remote Similarity	NPC54627
0.5165	Remote Similarity	NPC249817
0.5147	Remote Similarity	NPC27765
0.5147	Remote Similarity	NPC122418
0.5147	Remote Similarity	NPC491014
0.5135	Remote Similarity	NPC86372
0.5132	Remote Similarity	NPC259733
0.5132	Remote Similarity	NPC158371
0.5132	Remote Similarity	NPC207922
0.5132	Remote Similarity	NPC228784
0.5132	Remote Similarity	NPC324341
0.5132	Remote Similarity	NPC601810
0.5109	Remote Similarity	NPC304110
0.5109	Remote Similarity	NPC27518
0.5109	Remote Similarity	NPC611516
0.5106	Remote Similarity	NPC479745
0.507	Remote Similarity	NPC40394
0.5067	Remote Similarity	NPC64872
0.5067	Remote Similarity	NPC84319
0.5067	Remote Similarity	NPC25906
0.5067	Remote Similarity	NPC52021
0.5067	Remote Similarity	NPC112866
0.5067	Remote Similarity	NPC599947

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC607851 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6761
0.1-0.2	2338
0.2-0.3	46
0.3-0.4	3
0.4-0.5	1
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
0.5479	Remote Similarity	NPD7645	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