NPASS Compound

Natural Product: NPC605663

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 99104 0 0 0 0 0 0 0 0999 V2000 -7.4899 -2.2893 0.0502 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4372 -1.2235 -0.2581 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5420 -1.7765 -1.2925 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2134 -0.0027 -0.6941 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2360 1.0952 -0.9170 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4696 1.4485 0.3455 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.5393 2.0420 1.2352 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7785 1.5876 2.3586 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2467 3.1188 0.7470 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5511 2.5833 0.0316 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1613 2.3620 0.5039 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6373 1.0060 0.0916 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7392 0.8622 -1.3763 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4646 0.0228 0.8780 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9289 -1.0521 1.4190 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4950 -1.4345 1.3384 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8266 -0.5635 0.3600 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6562 -0.8475 0.1725 C 0 0 1 0 0 0 0 0 0 0 0 0 1.3667 -0.5528 1.4231 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8693 -2.3017 -0.1636 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3230 -2.5979 -0.4063 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3420 -3.8651 -1.0459 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0750 -1.5656 -1.1701 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1784 -0.9977 -0.4724 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4928 -1.1338 -0.8106 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8024 -1.8043 -1.8081 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5220 -0.4753 0.0258 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8019 -0.5786 -0.2603 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8685 0.0459 0.5226 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6469 0.7991 1.6301 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7282 1.3617 2.3177 C 0 0 0 0 0 0 0 0 0 0 0 0 11.0192 1.1700 1.8976 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1084 1.7131 2.5562 O 0 0 0 0 0 0 0 0 0 0 0 0 11.2370 0.4008 0.7677 C 0 0 0 0 0 0 0 0 0 0 0 0 10.1805 -0.1513 0.0925 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2309 -0.5056 -1.7956 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1058 0.7041 -2.1064 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8469 -1.0362 -3.1940 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0366 -0.0588 -1.0351 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9939 1.3880 -0.6648 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3078 1.8533 -0.1325 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1659 0.8568 0.5740 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2760 1.2740 2.0294 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8911 0.2958 1.0760 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8095 -0.8755 1.0619 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0780 -3.1041 0.6558 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2498 -1.7616 0.6867 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0070 -2.6197 -0.8569 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9670 -2.7125 -1.7593 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4638 -1.0654 -2.1395 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5011 -1.9610 -0.9590 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8273 -0.1873 -1.5892 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8443 0.2932 0.1887 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5648 0.9134 -1.7495 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8118 2.0211 -1.1712 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8042 3.7134 1.3306 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6580 2.8823 -1.0349 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8861 3.5440 0.5649 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2103 2.4821 1.6284 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4819 3.1823 0.1738 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3242 1.7106 -1.8496 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8017 0.8642 -1.9508 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2870 -0.0418 -1.7148 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5576 -1.7203 1.9769 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3792 -2.5079 1.0593 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1247 -1.3618 2.3940 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2585 -0.8761 -0.6474 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3600 -1.0976 1.5261 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8042 -0.9946 2.2708 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6475 0.5007 1.6016 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5700 -2.9606 0.7004 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3061 -2.6214 -1.0429 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8836 -2.8001 0.5543 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2908 -4.0151 -1.2862 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5878 -2.1214 -2.0173 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2368 0.1048 0.8901 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0399 -1.1735 -1.1414 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6493 0.9751 1.9960 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5610 1.9671 3.2071 H 0 0 0 0 0 0 0 0 0 0 0 0 12.7984 2.1868 1.9900 H 0 0 0 0 0 0 0 0 0 0 0 0 12.2765 0.2606 0.4492 H 0 0 0 0 0 0 0 0 0 0 0 0 10.3558 -0.7449 -0.7787 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5812 1.2700 -2.9080 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4037 1.2809 -1.2380 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0027 0.2651 -2.6442 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8600 -0.5822 -3.4464 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6289 -0.8130 -3.9288 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7008 -2.1274 -3.1651 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1986 -0.1774 -1.7707 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8644 1.7053 -0.0153 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1817 1.9601 -1.6212 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0601 2.7220 0.5567 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9196 2.3526 -0.9139 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2377 2.4066 2.0132 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4105 1.0044 2.6535 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2103 0.9929 2.5160 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9308 0.6387 2.1845 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7094 -0.5780 1.6976 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4487 -1.7748 1.6074 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 1 7 8 2 0 7 9 1 0 6 10 1 0 10 11 1 0 11 12 1 0 12 13 1 6 12 14 1 0 14 15 2 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 1 18 20 1 0 20 21 1 0 21 22 1 0 21 23 1 0 23 24 1 0 24 25 1 0 25 26 2 0 25 27 1 0 27 28 2 0 28 29 1 0 29 30 2 0 30 31 1 0 31 32 2 0 32 33 1 0 32 34 1 0 34 35 2 0 23 36 1 0 36 37 1 0 36 38 1 0 36 39 1 0 39 40 1 0 40 41 1 0 41 42 1 0 42 43 1 1 14 44 1 0 44 45 1 0 45 2 1 0 44 6 1 0 42 12 1 0 42 17 1 0 39 18 1 0 35 29 1 0 1 46 1 0 1 47 1 0 1 48 1 0 3 49 1 0 3 50 1 0 3 51 1 0 4 52 1 0 4 53 1 0 5 54 1 0 5 55 1 0 9 56 1 0 10 57 1 0 10 58 1 0 11 59 1 0 11 60 1 0 13 61 1 0 13 62 1 0 13 63 1 0 15 64 1 0 16 65 1 0 16 66 1 0 17 67 1 0 19 68 1 0 19 69 1 0 19 70 1 0 20 71 1 0 20 72 1 0 21 73 1 1 22 74 1 0 23 75 1 6 27 76 1 0 28 77 1 0 30 78 1 0 31 79 1 0 33 80 1 0 34 81 1 0 35 82 1 0 37 83 1 0 37 84 1 0 37 85 1 0 38 86 1 0 38 87 1 0 38 88 1 0 39 89 1 6 40 90 1 0 40 91 1 0 41 92 1 0 41 93 1 0 43 94 1 0 43 95 1 0 43 96 1 0 44 97 1 0 45 98 1 0 45 99 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 NPC605663 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	7530
0.1-0.2	36845
0.2-0.3	4677
0.3-0.4	507
0.4-0.5	205
0.5-0.6	58
0.6-0.7	12
0.7-0.8	0
0.8-0.85	4
0.85-0.9	4
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8706	High Similarity	NPC171007
0.8706	High Similarity	NPC190849
0.8571	High Similarity	NPC601567
0.8571	High Similarity	NPC606631
0.8111	Intermediate Similarity	NPC304110
0.8111	Intermediate Similarity	NPC25491
0.8111	Intermediate Similarity	NPC27518
0.8111	Intermediate Similarity	NPC611516
0.7978	Intermediate Similarity	NPC22676
0.7447	Intermediate Similarity	NPC178093
0.7368	Intermediate Similarity	NPC482051
0.7368	Intermediate Similarity	NPC324798
0.7368	Intermediate Similarity	NPC479742
0.7312	Intermediate Similarity	NPC198621
0.7312	Intermediate Similarity	NPC216940
0.701	Intermediate Similarity	NPC610795
0.7	Intermediate Similarity	NPC481234
0.7	Intermediate Similarity	NPC118033
0.7	Intermediate Similarity	NPC479431
0.6979	Remote Similarity	NPC132126
0.6768	Remote Similarity	NPC479745
0.6531	Remote Similarity	NPC172311
0.6531	Remote Similarity	NPC482052
0.6495	Remote Similarity	NPC101863
0.6429	Remote Similarity	NPC262970
0.6238	Remote Similarity	NPC479739
0.62	Remote Similarity	NPC479744
0.6122	Remote Similarity	NPC477874
0.6058	Remote Similarity	NPC479740
0.6058	Remote Similarity	NPC479741
0.604	Remote Similarity	NPC488214
0.5926	Remote Similarity	NPC53520
0.5922	Remote Similarity	NPC479747
0.5922	Remote Similarity	NPC479746
0.5922	Remote Similarity	NPC482049
0.5922	Remote Similarity	NPC482050
0.587	Remote Similarity	NPC233012
0.5842	Remote Similarity	NPC488215
0.5795	Remote Similarity	NPC120840
0.5761	Remote Similarity	NPC230151
0.5758	Remote Similarity	NPC43353
0.5644	Remote Similarity	NPC475627
0.5556	Remote Similarity	NPC206232
0.5556	Remote Similarity	NPC14515
0.5545	Remote Similarity	NPC475138
0.5534	Remote Similarity	NPC477873
0.5524	Remote Similarity	NPC606782
0.5506	Remote Similarity	NPC110308
0.55	Remote Similarity	NPC485587
0.5495	Remote Similarity	NPC481235
0.5446	Remote Similarity	NPC173569
0.5435	Remote Similarity	NPC296164
0.5393	Remote Similarity	NPC84319
0.5393	Remote Similarity	NPC52021
0.5393	Remote Similarity	NPC599947
0.534	Remote Similarity	NPC26045
0.5333	Remote Similarity	NPC231063
0.5333	Remote Similarity	NPC282395
0.5333	Remote Similarity	NPC481360
0.53	Remote Similarity	NPC470617
0.53	Remote Similarity	NPC470616
0.5283	Remote Similarity	NPC54627
0.5283	Remote Similarity	NPC249817
0.5281	Remote Similarity	NPC480946
0.5281	Remote Similarity	NPC130577
0.5281	Remote Similarity	NPC142415
0.5281	Remote Similarity	NPC102683
0.5275	Remote Similarity	NPC200752
0.5271	Remote Similarity	NPC488210
0.5222	Remote Similarity	NPC282616
0.52	Remote Similarity	NPC283849
0.5185	Remote Similarity	NPC475482
0.5165	Remote Similarity	NPC158141
0.5164	Remote Similarity	NPC488211
0.5146	Remote Similarity	NPC248287
0.5146	Remote Similarity	NPC234548
0.5146	Remote Similarity	NPC155192
0.5143	Remote Similarity	NPC485423
0.5109	Remote Similarity	NPC298554
0.5096	Remote Similarity	NPC284807
0.5055	Remote Similarity	NPC270768
0.5055	Remote Similarity	NPC59263
0.5055	Remote Similarity	NPC210106
0.5055	Remote Similarity	NPC275809
0.5055	Remote Similarity	NPC156981
0.505	Remote Similarity	NPC28198
0.505	Remote Similarity	NPC476123
0.505	Remote Similarity	NPC606107
0.5045	Remote Similarity	NPC469945

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC605663 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3594
0.1-0.2	5446
0.2-0.3	103
0.3-0.4	6
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
0.5524	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