NPASS Compound

Natural Product: NPC606745

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 43 44 0 0 0 0 0 0 0 0999 V2000 2.7725 2.0070 -0.8588 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5478 1.9707 -0.4800 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6404 3.1601 -0.5801 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9884 4.3538 -0.6985 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6748 2.6907 -0.5175 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5826 1.2703 -0.7638 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7981 0.5730 -0.3818 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5792 0.7144 0.6260 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4738 1.7281 1.7420 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4496 -0.4836 1.0323 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9651 -1.7272 0.2484 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4537 -1.5520 0.3085 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6054 -1.9268 -0.6198 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1807 -2.6255 -1.8427 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8108 -1.4609 -0.6653 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1284 -0.3911 0.3140 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5633 -0.2387 0.4292 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2216 -0.5214 1.5973 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7011 -0.3578 1.6952 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5186 -0.9166 2.5548 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6081 0.9668 0.1060 C 0 0 1 0 0 0 0 0 0 0 0 0 3.5263 1.2377 -0.8449 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1851 2.9568 -1.2784 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3110 1.1911 -1.8237 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2104 -0.1037 -1.1982 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7704 1.3915 2.5115 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4755 1.8701 2.2005 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1659 2.7168 1.3514 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3413 -0.6883 2.0991 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4679 -0.2878 0.7419 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2441 -2.6511 0.7689 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3565 -1.7260 -0.7556 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1094 -1.0809 1.2493 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3555 -3.3039 -2.2034 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0774 -3.2106 -1.5670 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3754 -1.8599 -2.6054 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9932 -1.1734 -1.7225 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4283 -2.3740 -0.4880 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8235 -0.7469 1.3123 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0773 0.2333 0.8592 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2219 -1.3259 1.8485 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9239 0.2376 2.6278 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3431 1.4644 1.1127 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 3 5 1 0 5 6 1 0 6 7 1 0 7 8 2 0 8 9 1 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 13 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 18 20 2 0 16 21 1 0 21 2 1 0 21 6 1 0 1 22 1 0 1 23 1 0 6 24 1 6 7 25 1 0 9 26 1 0 9 27 1 0 9 28 1 0 10 29 1 0 10 30 1 0 11 31 1 0 11 32 1 0 12 33 1 0 14 34 1 0 14 35 1 0 14 36 1 0 15 37 1 0 15 38 1 0 16 39 1 1 19 40 1 0 19 41 1 0 19 42 1 0 21 43 1 1 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 NPC606745 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	22394
0.1-0.2	23838
0.2-0.3	2988
0.3-0.4	438
0.4-0.5	130
0.5-0.6	44
0.6-0.7	12
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC171204
0.878	High Similarity	NPC611318
0.7347	Intermediate Similarity	NPC470755
0.7347	Intermediate Similarity	NPC298801
0.7045	Intermediate Similarity	NPC97516
0.66	Remote Similarity	NPC481909
0.66	Remote Similarity	NPC158756
0.66	Remote Similarity	NPC601035
0.6226	Remote Similarity	NPC469910
0.6222	Remote Similarity	NPC58956
0.6222	Remote Similarity	NPC163003
0.6222	Remote Similarity	NPC295633
0.6222	Remote Similarity	NPC269206
0.6182	Remote Similarity	NPC481911
0.6122	Remote Similarity	NPC476028
0.6122	Remote Similarity	NPC270126
0.6038	Remote Similarity	NPC605339
0.5849	Remote Similarity	NPC281132
0.5636	Remote Similarity	NPC131669
0.5625	Remote Similarity	NPC167881
0.5625	Remote Similarity	NPC98557
0.5577	Remote Similarity	NPC151770
0.5577	Remote Similarity	NPC250940
0.5577	Remote Similarity	NPC165383
0.5577	Remote Similarity	NPC169575
0.5556	Remote Similarity	NPC266957
0.5556	Remote Similarity	NPC482131
0.549	Remote Similarity	NPC609300
0.549	Remote Similarity	NPC610417
0.5472	Remote Similarity	NPC473390
0.5472	Remote Similarity	NPC194871
0.5472	Remote Similarity	NPC488296
0.5455	Remote Similarity	NPC482130
0.5455	Remote Similarity	NPC482128
0.5455	Remote Similarity	NPC482129
0.5385	Remote Similarity	NPC470256
0.5385	Remote Similarity	NPC50637
0.5385	Remote Similarity	NPC476355
0.537	Remote Similarity	NPC178702
0.5357	Remote Similarity	NPC481806
0.5357	Remote Similarity	NPC269509
0.5357	Remote Similarity	NPC17585
0.5283	Remote Similarity	NPC116177
0.5283	Remote Similarity	NPC7563
0.5273	Remote Similarity	NPC482126
0.5273	Remote Similarity	NPC320630
0.5273	Remote Similarity	NPC250315
0.5263	Remote Similarity	NPC40746
0.52	Remote Similarity	NPC140287
0.5179	Remote Similarity	NPC307411
0.5172	Remote Similarity	NPC134725
0.5172	Remote Similarity	NPC48657
0.5172	Remote Similarity	NPC483718
0.5098	Remote Similarity	NPC301477
0.5098	Remote Similarity	NPC25684
0.5098	Remote Similarity	NPC488306
0.5094	Remote Similarity	NPC600792
0.5094	Remote Similarity	NPC610427
0.5091	Remote Similarity	NPC473619
0.5091	Remote Similarity	NPC272814
0.5088	Remote Similarity	NPC482127

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC606745 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7201
0.1-0.2	1903
0.2-0.3	40
0.3-0.4	6
0.4-0.5	0
0.5-0.6	0
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
		NPD

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