NPASS Compound

Natural Product: NPC604652

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 45 0 0 0 0 0 0 0 0999 V2000 4.7378 1.9633 -0.2152 N 0 0 0 0 0 0 0 0 0 0 0 0 5.3549 0.9038 -0.9519 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4568 -0.3121 -0.9463 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1844 -0.8154 0.4557 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3891 0.3558 1.5180 S 0 0 0 0 0 0 0 0 0 0 0 0 1.7473 0.8566 1.1249 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6613 -0.1586 1.2357 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5972 0.4067 0.9068 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3570 -0.7445 0.7166 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.7080 -0.4641 0.3258 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.5833 -1.4322 -0.0253 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7582 -0.8940 -0.3399 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.6579 0.4273 -0.1967 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5718 1.4320 -0.3922 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8671 1.1137 -0.8172 N 0 0 0 0 0 0 0 0 0 0 0 0 -5.1483 2.7043 -0.1543 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.8887 2.9531 0.2536 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9763 1.9598 0.4495 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.3700 0.6909 0.2210 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5487 -1.4062 -0.3768 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8873 -2.7283 -0.5732 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8511 -1.2808 0.2499 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0695 -2.5087 0.8680 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3217 2.1584 0.6303 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6032 2.8239 -0.7919 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3368 0.6400 -0.5415 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5105 1.1604 -2.0319 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5595 -0.1159 -1.5328 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0219 -1.1192 -1.4673 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6369 -1.7481 0.3753 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2047 -1.1232 0.8561 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7581 1.2982 0.0790 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5091 1.7686 1.7546 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5741 -0.4863 2.2785 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2686 -1.3637 1.6303 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3981 -2.5089 -0.0601 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6179 0.9328 -0.1275 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0942 1.0541 -1.8256 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6258 3.9885 0.4220 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5754 -0.8108 -1.3146 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2906 -2.7844 -1.4882 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5927 -1.0338 -0.5371 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7089 -3.2688 0.3559 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 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 14 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 9 20 1 0 20 21 1 0 20 22 1 0 22 23 1 0 22 7 1 0 19 10 1 0 19 13 1 0 1 24 1 0 1 25 1 0 2 26 1 0 2 27 1 0 3 28 1 0 3 29 1 0 4 30 1 0 4 31 1 0 6 32 1 0 6 33 1 0 7 34 1 1 9 35 1 1 11 36 1 0 15 37 1 0 15 38 1 0 17 39 1 0 20 40 1 6 21 41 1 0 22 42 1 6 23 43 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 NPC604652 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	34107
0.1-0.2	15566
0.2-0.3	65
0.3-0.4	48
0.4-0.5	27
0.5-0.6	22
0.6-0.7	17
0.7-0.8	2
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	NPC328479
0.8	Intermediate Similarity	NPC136349
0.8	Intermediate Similarity	NPC219313
0.75	Intermediate Similarity	NPC324484
0.7385	Intermediate Similarity	NPC185991
0.7385	Intermediate Similarity	NPC321814
0.6957	Remote Similarity	NPC324198
0.6957	Remote Similarity	NPC326529
0.6957	Remote Similarity	NPC319100
0.6885	Remote Similarity	NPC156461
0.6885	Remote Similarity	NPC107374
0.6885	Remote Similarity	NPC600382
0.6885	Remote Similarity	NPC612067
0.6857	Remote Similarity	NPC130586
0.6833	Remote Similarity	NPC317821
0.6667	Remote Similarity	NPC174802
0.6575	Remote Similarity	NPC606410
0.6486	Remote Similarity	NPC316618
0.6486	Remote Similarity	NPC323091
0.6316	Remote Similarity	NPC484199
0.6234	Remote Similarity	NPC484196
0.6027	Remote Similarity	NPC195140
0.6	Remote Similarity	NPC229974
0.5758	Remote Similarity	NPC209525
0.5758	Remote Similarity	NPC161659
0.5714	Remote Similarity	NPC325906
0.5714	Remote Similarity	NPC606116
0.5672	Remote Similarity	NPC609472
0.5616	Remote Similarity	NPC121222
0.5333	Remote Similarity	NPC472816
0.5333	Remote Similarity	NPC164952
0.5333	Remote Similarity	NPC600171
0.5319	Remote Similarity	NPC90902
0.5316	Remote Similarity	NPC481375
0.5263	Remote Similarity	NPC302778
0.5263	Remote Similarity	NPC329404
0.5263	Remote Similarity	NPC212551
0.5217	Remote Similarity	NPC21461
0.5205	Remote Similarity	NPC261595
0.5205	Remote Similarity	NPC85689
0.5147	Remote Similarity	NPC33996
0.5143	Remote Similarity	NPC309832
0.5125	Remote Similarity	NPC161224
0.5068	Remote Similarity	NPC605318
0.5067	Remote Similarity	NPC239737

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC604652 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6460
0.1-0.2	2524
0.2-0.3	87
0.3-0.4	45
0.4-0.5	19
0.5-0.6	8
0.6-0.7	4
0.7-0.8	2
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8	Intermediate Similarity	NPD548	Clinical (unspecified phase)
0.7385	Intermediate Similarity	NPD283	Phase 4
0.7164	Intermediate Similarity	NPD4171	Clinical (unspecified phase)
0.6957	Remote Similarity	NPD338	Approved
0.6885	Remote Similarity	NPD249	Phase 4
0.6885	Remote Similarity	NPD250	Phase 4
0.6667	Remote Similarity	NPD339	Phase 2
0.5714	Remote Similarity	NPD1777	Phase 4
0.557	Remote Similarity	NPD1776	Approved
0.5541	Remote Similarity	NPD1369	Phase 2
0.5333	Remote Similarity	NPD242	Phase 4
0.5319	Remote Similarity	NPD4716	Approved
0.5205	Remote Similarity	NPD247	Clinical (unspecified phase)
0.5143	Remote Similarity	NPD193	Phase 2
0.5122	Remote Similarity	NPD1732	Phase 3

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