NPASS Compound

Natural Product: NPC602065

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 66 71 0 0 0 0 0 0 0 0999 V2000 5.8893 4.9775 1.3282 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0700 3.9050 0.9930 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0098 3.4959 1.7810 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2219 2.4069 1.3868 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4944 1.7417 0.2222 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6984 0.6043 -0.2416 C 0 0 1 0 0 0 0 0 0 0 0 0 3.5224 -0.4872 -0.6065 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9014 -1.5992 -1.1553 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6156 -2.5011 -1.9417 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9642 -3.5904 -2.4666 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6589 -4.5004 -3.2528 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6207 -3.7623 -2.2011 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9042 -2.8772 -1.4249 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5613 -1.7655 -0.8872 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7414 -0.8434 -0.0588 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1276 -1.6048 0.8866 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3856 -2.2860 1.9640 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7436 -2.2870 2.2169 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4448 -2.9973 2.8364 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8058 -3.0302 2.6319 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6761 -3.7187 3.4639 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3231 -2.3604 1.5704 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4920 -1.6486 0.6974 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9982 -0.9556 -0.3956 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3803 -0.5972 -0.4746 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5212 0.8432 -0.8011 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7471 1.4034 -1.7932 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8997 2.7627 -2.0792 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8073 3.5541 -1.3907 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9647 4.9048 -1.6690 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5601 2.9805 -0.4164 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4793 3.7608 0.2883 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4122 1.6215 -0.1255 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0669 -0.8716 0.8475 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5250 -0.0572 1.8412 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7717 -2.3235 1.2481 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5340 0.2325 0.6153 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7354 1.4051 0.7020 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5534 2.1654 -0.5456 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3451 3.2341 -0.1812 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8685 5.0198 1.0831 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8339 4.0434 2.6801 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4272 2.1555 2.0560 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2445 0.9368 -1.2336 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6776 -2.2949 -2.1057 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1800 -5.2895 -2.8456 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1495 -4.6388 -2.6381 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1451 -3.0285 -1.2287 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0815 -0.3152 -0.8104 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1372 -2.0274 3.1254 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0562 -3.5358 3.6850 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0935 -4.5878 3.0972 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8791 -1.2216 -1.2503 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0167 0.8379 -2.3707 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2901 3.2072 -2.8620 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8842 5.3541 -1.5666 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4617 3.7509 0.0415 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0580 1.2573 0.6687 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1469 -0.7932 0.7401 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8230 0.5512 1.4529 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9084 -2.9321 0.3247 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4103 -2.6417 2.0783 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8224 0.0007 1.6546 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6334 1.7061 -0.2364 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7934 1.6469 -1.4867 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1559 3.5043 -0.8369 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 1 0 10 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 16 17 2 0 17 18 1 0 17 19 1 0 19 20 2 0 20 21 1 0 20 22 1 0 22 23 2 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 2 0 27 28 1 0 28 29 2 0 29 30 1 0 29 31 1 0 31 32 1 0 31 33 2 0 25 34 1 0 34 35 1 0 34 36 1 0 15 37 1 0 37 38 1 0 5 39 1 0 39 40 2 0 40 2 1 0 37 6 1 0 14 8 1 0 23 16 1 0 33 26 1 0 36 22 1 0 1 41 1 0 3 42 1 0 4 43 1 0 6 44 1 6 9 45 1 0 11 46 1 0 12 47 1 0 13 48 1 0 15 49 1 6 18 50 1 0 19 51 1 0 21 52 1 0 25 53 1 6 27 54 1 0 28 55 1 0 30 56 1 0 32 57 1 0 33 58 1 0 34 59 1 6 35 60 1 0 36 61 1 0 36 62 1 0 37 63 1 1 38 64 1 0 39 65 1 0 40 66 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 NPC602065 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	22434
0.1-0.2	24027
0.2-0.3	3035
0.3-0.4	221
0.4-0.5	57
0.5-0.6	38
0.6-0.7	20
0.7-0.8	0
0.8-0.85	0
0.85-0.9	3
0.9-0.95	4
0.95-1	7

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC70409
1.0	High Similarity	NPC204770
1.0	High Similarity	NPC600551
1.0	High Similarity	NPC601980
1.0	High Similarity	NPC611024
0.9667	High Similarity	NPC313116
0.9667	High Similarity	NPC603340
0.9167	High Similarity	NPC601999
0.9062	High Similarity	NPC600630
0.9062	High Similarity	NPC607896
0.9062	High Similarity	NPC611369
0.8906	High Similarity	NPC601997
0.8906	High Similarity	NPC609211
0.8906	High Similarity	NPC610665
0.7969	Intermediate Similarity	NPC58190
0.7969	Intermediate Similarity	NPC108811
0.7969	Intermediate Similarity	NPC170103
0.7969	Intermediate Similarity	NPC236202
0.7969	Intermediate Similarity	NPC262911
0.7969	Intermediate Similarity	NPC202742
0.7846	Intermediate Similarity	NPC246202
0.7846	Intermediate Similarity	NPC224161
0.7846	Intermediate Similarity	NPC46335
0.7846	Intermediate Similarity	NPC279406
0.7846	Intermediate Similarity	NPC486519
0.7083	Intermediate Similarity	NPC278548
0.6912	Remote Similarity	NPC82917
0.6806	Remote Similarity	NPC211561
0.6618	Remote Similarity	NPC96576
0.6575	Remote Similarity	NPC226809
0.6338	Remote Similarity	NPC294558
0.6338	Remote Similarity	NPC18185
0.6338	Remote Similarity	NPC263940
0.6296	Remote Similarity	NPC86630
0.625	Remote Similarity	NPC147743
0.625	Remote Similarity	NPC4809
0.625	Remote Similarity	NPC73517
0.622	Remote Similarity	NPC106601
0.622	Remote Similarity	NPC151474
0.6184	Remote Similarity	NPC302549
0.6154	Remote Similarity	NPC306267
0.6145	Remote Similarity	NPC212614
0.6145	Remote Similarity	NPC205613
0.6027	Remote Similarity	NPC184245
0.6027	Remote Similarity	NPC187801
0.6027	Remote Similarity	NPC610920
0.5972	Remote Similarity	NPC277331
0.5972	Remote Similarity	NPC100482
0.597	Remote Similarity	NPC178054
0.5938	Remote Similarity	NPC261619
0.5938	Remote Similarity	NPC61477
0.5938	Remote Similarity	NPC78770
0.5938	Remote Similarity	NPC219876
0.5938	Remote Similarity	NPC126029
0.5938	Remote Similarity	NPC15658
0.593	Remote Similarity	NPC159526
0.5875	Remote Similarity	NPC135021
0.5854	Remote Similarity	NPC9309
0.5823	Remote Similarity	NPC20050
0.5769	Remote Similarity	NPC46283
0.5769	Remote Similarity	NPC469944
0.5647	Remote Similarity	NPC78074
0.5625	Remote Similarity	NPC207179
0.5625	Remote Similarity	NPC167571
0.5625	Remote Similarity	NPC278552
0.5618	Remote Similarity	NPC478617
0.557	Remote Similarity	NPC134911
0.5469	Remote Similarity	NPC601844
0.5465	Remote Similarity	NPC478340
0.5443	Remote Similarity	NPC272552
0.5443	Remote Similarity	NPC226108
0.5443	Remote Similarity	NPC322899
0.5422	Remote Similarity	NPC471404
0.5402	Remote Similarity	NPC478337
0.5402	Remote Similarity	NPC478338
0.5395	Remote Similarity	NPC165483
0.5366	Remote Similarity	NPC478616
0.5366	Remote Similarity	NPC478339
0.5309	Remote Similarity	NPC44192
0.5256	Remote Similarity	NPC155564
0.5227	Remote Similarity	NPC479793
0.5111	Remote Similarity	NPC479794
0.5065	Remote Similarity	NPC20757
0.5065	Remote Similarity	NPC227516

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC602065 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4771
0.1-0.2	4309
0.2-0.3	60
0.3-0.4	8
0.4-0.5	0
0.5-0.6	2
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
0.5938	Remote Similarity	NPD1612	Clinical (unspecified phase)
0.5938	Remote Similarity	NPD1613	Phase 4

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