NPASS Compound

Natural Product: NPC605787

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 39 41 0 0 0 0 0 0 0 0999 V2000 -7.0558 0.5522 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3378 0.6170 -0.2660 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9518 0.5312 -0.3197 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3604 0.6069 -1.5662 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9855 0.5253 -1.6575 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2007 0.3685 -0.5089 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8274 0.2865 -0.5949 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3088 0.3568 -1.7311 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0559 0.1317 0.5413 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4038 0.0448 0.4469 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1595 0.7785 1.3373 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5558 0.7109 1.2657 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1895 -0.0733 0.3242 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5686 -0.1739 0.2127 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4678 0.5076 1.0411 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4100 -0.8056 -0.5648 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0431 -1.5954 -1.5131 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2554 -2.3408 -2.4180 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0338 -0.7441 -0.5004 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7167 0.0640 1.7514 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0260 0.1457 1.7950 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7829 0.2919 0.7412 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1592 0.3768 0.7982 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1321 0.4704 0.6879 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9287 1.4480 1.5737 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6870 -0.3320 1.5005 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9403 0.7279 -2.4708 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4624 0.5779 -2.6045 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7411 1.4157 2.1030 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1708 1.2813 1.9584 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0755 1.5235 1.2721 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4725 0.5694 0.5491 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6065 -0.0599 1.9662 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6274 -3.1023 -1.8751 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8981 -2.9284 -3.1052 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5428 -1.6925 -2.9717 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4488 -1.3235 -1.2036 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1249 -0.0579 2.6576 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6264 0.3192 1.7589 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 7 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 1 0 13 16 1 0 16 17 1 0 17 18 1 0 16 19 2 0 9 20 2 0 20 21 1 0 21 22 1 0 22 23 2 0 23 3 1 0 22 6 1 0 19 10 1 0 1 24 1 0 1 25 1 0 1 26 1 0 4 27 1 0 5 28 1 0 11 29 1 0 12 30 1 0 15 31 1 0 15 32 1 0 15 33 1 0 18 34 1 0 18 35 1 0 18 36 1 0 19 37 1 0 20 38 1 0 23 39 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 NPC605787 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	33575
0.1-0.2	14259
0.2-0.3	1580
0.3-0.4	289
0.4-0.5	102
0.5-0.6	33
0.6-0.7	8
0.7-0.8	0
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC185607
0.8269	Intermediate Similarity	NPC602183
0.8125	Intermediate Similarity	NPC182428
0.7885	Intermediate Similarity	NPC471590
0.7857	Intermediate Similarity	NPC185401
0.76	Intermediate Similarity	NPC195919
0.75	Intermediate Similarity	NPC216314
0.7037	Intermediate Similarity	NPC181124
0.7037	Intermediate Similarity	NPC136095
0.6786	Remote Similarity	NPC12377
0.6441	Remote Similarity	NPC254741
0.6415	Remote Similarity	NPC120924
0.6316	Remote Similarity	NPC148497
0.6271	Remote Similarity	NPC153008
0.625	Remote Similarity	NPC479067
0.6167	Remote Similarity	NPC478213
0.6102	Remote Similarity	NPC602689
0.5862	Remote Similarity	NPC186507
0.5789	Remote Similarity	NPC113089
0.5789	Remote Similarity	NPC474264
0.5738	Remote Similarity	NPC110086
0.569	Remote Similarity	NPC603503
0.5667	Remote Similarity	NPC200316
0.5593	Remote Similarity	NPC209560
0.5593	Remote Similarity	NPC490700
0.5522	Remote Similarity	NPC488570
0.5517	Remote Similarity	NPC299923
0.5469	Remote Similarity	NPC260640
0.5439	Remote Similarity	NPC182842
0.5439	Remote Similarity	NPC223354
0.5429	Remote Similarity	NPC45165
0.5424	Remote Similarity	NPC474340
0.5405	Remote Similarity	NPC601607
0.5397	Remote Similarity	NPC35544
0.5352	Remote Similarity	NPC478528
0.5333	Remote Similarity	NPC121522
0.5286	Remote Similarity	NPC487214
0.5254	Remote Similarity	NPC605229
0.5246	Remote Similarity	NPC602344
0.5217	Remote Similarity	NPC25547
0.5205	Remote Similarity	NPC5840
0.5167	Remote Similarity	NPC10467
0.5167	Remote Similarity	NPC116632
0.5167	Remote Similarity	NPC333691
0.5152	Remote Similarity	NPC488135
0.5143	Remote Similarity	NPC607700
0.5135	Remote Similarity	NPC78071
0.5082	Remote Similarity	NPC609386
0.5079	Remote Similarity	NPC80710
0.5079	Remote Similarity	NPC139364

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC605787 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5257
0.1-0.2	3773
0.2-0.3	113
0.3-0.4	5
0.4-0.5	1
0.5-0.6	0
0.6-0.7	1
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
0.625	Remote Similarity	NPD2796	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