NPASS Compound

Natural Product: NPC606028

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 47 48 0 0 0 0 0 0 0 0999 V2000 6.8660 -1.6688 1.8135 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2455 -0.5070 1.1015 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2861 0.0743 0.2728 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0190 -0.4505 0.1446 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0605 0.1381 -0.6902 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7426 -0.4671 -0.7790 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7750 -0.0106 -1.5368 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4595 -0.6375 -1.6084 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2778 -1.6594 -0.8905 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5995 -0.1036 -2.4764 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7845 -0.9654 -2.3228 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8377 -2.0291 -3.0468 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8415 -0.6462 -1.4095 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8175 0.4200 -0.6636 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8443 0.8137 0.2828 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6993 1.9814 0.9923 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6384 2.4152 1.9118 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7716 1.6349 2.1227 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7206 2.0652 3.0462 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9447 0.4597 1.4269 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0862 -0.3180 1.6462 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2198 -1.5277 0.9039 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9708 0.0741 0.5173 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4572 1.2638 -1.3694 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7462 1.7989 -1.2397 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6746 1.2074 -0.4154 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9610 1.7112 -0.2639 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0022 -1.4781 2.4859 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7080 -2.0907 2.3982 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5692 -2.4532 1.0623 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7197 -1.3398 0.6872 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5093 -1.3636 -0.1885 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9457 0.8645 -2.1377 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7798 0.9638 -2.2965 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2375 -0.1483 -3.5470 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7300 -1.2990 -1.2996 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9466 1.0923 -0.7403 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8234 2.6328 0.8627 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5083 3.3376 2.4612 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7700 1.7267 4.0064 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1540 -2.0478 1.2170 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3527 -2.2059 1.1297 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1742 -1.3564 -0.1895 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1538 -0.8410 0.0069 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7423 1.7489 -2.0255 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0301 2.6753 -1.7782 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6090 1.3376 0.4153 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 2 0 11 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 18 20 1 0 20 21 1 0 21 22 1 0 20 23 2 0 5 24 2 0 24 25 1 0 25 26 2 0 26 27 1 0 26 3 1 0 23 15 1 0 1 28 1 0 1 29 1 0 1 30 1 0 4 31 1 0 6 32 1 0 7 33 1 0 10 34 1 0 10 35 1 0 13 36 1 0 14 37 1 0 16 38 1 0 17 39 1 0 19 40 1 0 22 41 1 0 22 42 1 0 22 43 1 0 23 44 1 0 24 45 1 0 25 46 1 0 27 47 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 NPC606028 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	18249
0.1-0.2	24075
0.2-0.3	6373
0.3-0.4	885
0.4-0.5	205
0.5-0.6	39
0.6-0.7	13
0.7-0.8	0
0.8-0.85	1
0.85-0.9	2
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC160900
0.8974	High Similarity	NPC71941
0.875	High Similarity	NPC106659
0.8158	Intermediate Similarity	NPC224814
0.7447	Intermediate Similarity	NPC304622
0.7381	Intermediate Similarity	NPC14007
0.7292	Intermediate Similarity	NPC474784
0.7105	Intermediate Similarity	NPC36108
0.7105	Intermediate Similarity	NPC233731
0.7105	Intermediate Similarity	NPC610203
0.7	Intermediate Similarity	NPC39793
0.6889	Remote Similarity	NPC60962
0.6667	Remote Similarity	NPC107588
0.6667	Remote Similarity	NPC137537
0.6596	Remote Similarity	NPC109083
0.6585	Remote Similarity	NPC78918
0.6585	Remote Similarity	NPC139617
0.6471	Remote Similarity	NPC253455
0.6458	Remote Similarity	NPC110313
0.6316	Remote Similarity	NPC246358
0.6154	Remote Similarity	NPC68269
0.6122	Remote Similarity	NPC70752
0.6087	Remote Similarity	NPC202474
0.6078	Remote Similarity	NPC189844
0.5957	Remote Similarity	NPC66905
0.5882	Remote Similarity	NPC276466
0.5882	Remote Similarity	NPC158949
0.5854	Remote Similarity	NPC159418
0.5854	Remote Similarity	NPC185738
0.5849	Remote Similarity	NPC269843
0.5833	Remote Similarity	NPC246704
0.5789	Remote Similarity	NPC471110
0.5745	Remote Similarity	NPC276014
0.5686	Remote Similarity	NPC83062
0.5686	Remote Similarity	NPC15621
0.566	Remote Similarity	NPC84076
0.566	Remote Similarity	NPC151167
0.56	Remote Similarity	NPC289459
0.56	Remote Similarity	NPC254659
0.549	Remote Similarity	NPC204466
0.549	Remote Similarity	NPC485638
0.549	Remote Similarity	NPC186898
0.5455	Remote Similarity	NPC71579
0.5455	Remote Similarity	NPC271785
0.5455	Remote Similarity	NPC51698
0.5435	Remote Similarity	NPC70744
0.5424	Remote Similarity	NPC472410
0.54	Remote Similarity	NPC148627
0.537	Remote Similarity	NPC60517
0.537	Remote Similarity	NPC146886
0.537	Remote Similarity	NPC135127
0.537	Remote Similarity	NPC20443
0.5333	Remote Similarity	NPC56332
0.5333	Remote Similarity	NPC10932
0.5333	Remote Similarity	NPC606519
0.52	Remote Similarity	NPC103823
0.5185	Remote Similarity	NPC213552
0.5185	Remote Similarity	NPC120225
0.5179	Remote Similarity	NPC482462
0.5128	Remote Similarity	NPC7097
0.5122	Remote Similarity	NPC203719
0.5106	Remote Similarity	NPC142985
0.5106	Remote Similarity	NPC127937

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC606028 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3121
0.1-0.2	5659
0.2-0.3	356
0.3-0.4	9
0.4-0.5	3
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	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD4379	Clinical (unspecified phase)
0.5854	Remote Similarity	NPD5536	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