NPASS Compound

Natural Product: NPC611955

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 27 28 0 0 0 0 0 0 0 0999 V2000 -2.9215 -0.3928 2.1552 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.9936 -0.0017 1.1103 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0747 -1.1798 0.8805 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0721 -0.8914 -0.1796 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0836 -1.3544 -1.4831 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9956 -0.8661 -2.1156 N 0 0 0 0 0 0 0 0 0 0 0 0 1.7229 -0.0974 -1.2833 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8993 0.6058 -1.4843 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4001 1.3105 -0.4097 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7674 1.3224 0.8149 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6026 0.6089 0.9642 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0578 -0.1103 -0.0691 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7665 0.3084 -0.1023 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0065 0.2161 -0.1022 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1132 0.7044 -1.2483 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3877 -0.3593 3.0656 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1349 -1.4107 1.9937 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4380 0.8830 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5348 -1.3436 1.8537 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7038 -2.0466 0.6347 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8589 -2.0015 -1.8777 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2679 -1.0377 -3.1196 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3819 0.5873 -2.4436 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3199 1.8768 -0.5201 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1836 1.8872 1.6475 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0781 0.5986 1.9233 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5873 0.9733 -2.0993 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 2 0 2 13 1 0 13 14 2 0 13 15 1 0 12 4 1 0 12 7 1 0 1 16 1 0 1 17 1 0 2 18 1 1 3 19 1 0 3 20 1 0 5 21 1 0 6 22 1 0 8 23 1 0 9 24 1 0 10 25 1 0 11 26 1 0 15 27 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 NPC611955 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	37015
0.1-0.2	11272
0.2-0.3	1137
0.3-0.4	279
0.4-0.5	111
0.5-0.6	21
0.6-0.7	15
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC149155
1.0	High Similarity	NPC203468
1.0	High Similarity	NPC110500
0.7872	Intermediate Similarity	NPC248041
0.7292	Intermediate Similarity	NPC480318
0.7255	Intermediate Similarity	NPC283219
0.7021	Intermediate Similarity	NPC78020
0.6939	Remote Similarity	NPC480321
0.68	Remote Similarity	NPC480324
0.68	Remote Similarity	NPC480325
0.68	Remote Similarity	NPC480322
0.6667	Remote Similarity	NPC480326
0.6667	Remote Similarity	NPC480316
0.6667	Remote Similarity	NPC45459
0.6667	Remote Similarity	NPC315491
0.6531	Remote Similarity	NPC315555
0.6531	Remote Similarity	NPC55772
0.6471	Remote Similarity	NPC480320
0.6471	Remote Similarity	NPC480323
0.64	Remote Similarity	NPC605329
0.6222	Remote Similarity	NPC96102
0.6038	Remote Similarity	NPC480317
0.5926	Remote Similarity	NPC267885
0.5909	Remote Similarity	NPC601214
0.5862	Remote Similarity	NPC602969
0.5745	Remote Similarity	NPC279081
0.5714	Remote Similarity	NPC111275
0.5667	Remote Similarity	NPC321708
0.56	Remote Similarity	NPC310665
0.5574	Remote Similarity	NPC606272
0.551	Remote Similarity	NPC84911
0.5417	Remote Similarity	NPC230869
0.537	Remote Similarity	NPC14113
0.537	Remote Similarity	NPC145885
0.537	Remote Similarity	NPC84827
0.5306	Remote Similarity	NPC29886
0.5294	Remote Similarity	NPC605863
0.5283	Remote Similarity	NPC59269
0.5263	Remote Similarity	NPC602670
0.5246	Remote Similarity	NPC605102
0.5185	Remote Similarity	NPC190296
0.5106	Remote Similarity	NPC105127
0.5098	Remote Similarity	NPC73767

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC611955 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4819
0.1-0.2	4031
0.2-0.3	222
0.3-0.4	63
0.4-0.5	5
0.5-0.6	4
0.6-0.7	4
0.7-0.8	1
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	NPD482	Phase 4
0.7292	Intermediate Similarity	NPD749	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD484	Phase 4
0.6222	Remote Similarity	NPD198	Clinical (unspecified phase)
0.6	Remote Similarity	NPD2094	Phase 2
0.6	Remote Similarity	NPD2095	Phase 2
0.5902	Remote Similarity	NPD2092	Phase 2
0.56	Remote Similarity	NPD786	Pre-clinical
0.5312	Remote Similarity	NPD2096	Phase 3
0.5075	Remote Similarity	NPD2091	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