NPASS Compound

Natural Product: NPC605284

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 42 41 0 0 0 0 0 0 0 0999 V2000 -4.0443 0.4875 1.4519 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2136 -0.9414 1.0174 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7355 -1.1024 -0.3787 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8180 -0.5192 -1.4497 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5416 -1.2279 -1.3656 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3795 -0.6630 -1.1579 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1824 0.7828 -0.9790 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5623 1.0825 0.3722 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7840 0.4177 0.5257 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7885 0.8438 -0.4929 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0979 0.1323 -0.2644 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6973 0.4157 1.0908 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0143 -0.3330 1.2483 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9303 0.1252 0.1924 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5210 1.2143 0.3147 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1316 -0.6501 -0.9262 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3640 0.5025 2.3447 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6402 1.0829 0.6311 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0602 0.8552 1.7425 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2413 -1.4792 1.1448 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8907 -1.4575 1.7623 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8454 -2.1878 -0.5942 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7422 -0.6320 -0.4623 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8063 0.5672 -1.3122 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3313 -0.7412 -2.4504 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5424 -2.3525 -1.4884 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4529 -1.3132 -1.1095 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1084 1.3303 -1.1513 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4589 1.1522 -1.7618 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2071 0.6762 1.1644 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4331 2.1600 0.5042 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6639 -0.6655 0.5216 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1571 0.7427 1.5305 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9329 1.9395 -0.5153 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4579 0.5180 -1.5223 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8638 -0.9680 -0.3410 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8467 0.3888 -1.0367 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0417 0.1187 1.9249 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9227 1.4971 1.1763 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8327 -1.4416 1.1831 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4057 -0.0714 2.2660 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5115 -0.2860 -1.8018 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 2 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 2 0 14 16 1 0 1 17 1 0 1 18 1 0 1 19 1 0 2 20 1 0 2 21 1 0 3 22 1 0 3 23 1 0 4 24 1 0 4 25 1 0 5 26 1 0 6 27 1 0 7 28 1 0 7 29 1 0 8 30 1 0 8 31 1 0 9 32 1 0 9 33 1 0 10 34 1 0 10 35 1 0 11 36 1 0 11 37 1 0 12 38 1 0 12 39 1 0 13 40 1 0 13 41 1 0 16 42 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 NPC605284 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	38061
0.1-0.2	9936
0.2-0.3	1420
0.3-0.4	230
0.4-0.5	82
0.5-0.6	48
0.6-0.7	32
0.7-0.8	6
0.8-0.85	5
0.85-0.9	8
0.9-0.95	0
0.95-1	10

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC281245
0.9615	High Similarity	NPC424
0.9615	High Similarity	NPC36061
0.9615	High Similarity	NPC69510
0.9615	High Similarity	NPC77272
0.9615	High Similarity	NPC290563
0.9615	High Similarity	NPC139029
0.9615	High Similarity	NPC281972
0.9615	High Similarity	NPC261831
0.9615	High Similarity	NPC87564
0.8889	High Similarity	NPC92114
0.8621	High Similarity	NPC154245
0.8621	High Similarity	NPC85813
0.8621	High Similarity	NPC223697
0.8621	High Similarity	NPC6095
0.8571	High Similarity	NPC95145
0.8571	High Similarity	NPC325642
0.8571	High Similarity	NPC65174
0.8276	Intermediate Similarity	NPC321062
0.8	Intermediate Similarity	NPC52955
0.8	Intermediate Similarity	NPC88966
0.8	Intermediate Similarity	NPC25417
0.8	Intermediate Similarity	NPC1813
0.7667	Intermediate Similarity	NPC5413
0.7667	Intermediate Similarity	NPC70387
0.7419	Intermediate Similarity	NPC59051
0.7308	Intermediate Similarity	NPC171736
0.7308	Intermediate Similarity	NPC301585
0.7308	Intermediate Similarity	NPC261080
0.7308	Intermediate Similarity	NPC132565
0.7308	Intermediate Similarity	NPC209970
0.7308	Intermediate Similarity	NPC216630
0.7308	Intermediate Similarity	NPC201844
0.7308	Intermediate Similarity	NPC301696
0.7308	Intermediate Similarity	NPC196924
0.7308	Intermediate Similarity	NPC307783
0.7308	Intermediate Similarity	NPC154186
0.7308	Intermediate Similarity	NPC149184
0.7308	Intermediate Similarity	NPC279026
0.7308	Intermediate Similarity	NPC113928
0.7308	Intermediate Similarity	NPC14227
0.7143	Intermediate Similarity	NPC180534
0.7143	Intermediate Similarity	NPC477201
0.7143	Intermediate Similarity	NPC611531
0.7097	Intermediate Similarity	NPC91495
0.7059	Intermediate Similarity	NPC606120
0.6923	Remote Similarity	NPC155263
0.68	Remote Similarity	NPC214610
0.68	Remote Similarity	NPC118968
0.68	Remote Similarity	NPC183424
0.68	Remote Similarity	NPC294085
0.6774	Remote Similarity	NPC149821
0.6757	Remote Similarity	NPC243532
0.6667	Remote Similarity	NPC106851
0.6667	Remote Similarity	NPC282788
0.6667	Remote Similarity	NPC34416
0.6667	Remote Similarity	NPC274927
0.6579	Remote Similarity	NPC68343
0.6579	Remote Similarity	NPC328089
0.6571	Remote Similarity	NPC225929
0.6538	Remote Similarity	NPC175342
0.6486	Remote Similarity	NPC179764
0.64	Remote Similarity	NPC268826
0.6316	Remote Similarity	NPC251042
0.6316	Remote Similarity	NPC255863
0.6316	Remote Similarity	NPC473863
0.6316	Remote Similarity	NPC174447
0.6316	Remote Similarity	NPC136164
0.6316	Remote Similarity	NPC122521
0.6316	Remote Similarity	NPC245947
0.625	Remote Similarity	NPC207292
0.6154	Remote Similarity	NPC318420
0.6154	Remote Similarity	NPC326268
0.6111	Remote Similarity	NPC487561
0.6061	Remote Similarity	NPC48162
0.6	Remote Similarity	NPC55023
0.6	Remote Similarity	NPC174368
0.6	Remote Similarity	NPC21844
0.5938	Remote Similarity	NPC8219
0.5897	Remote Similarity	NPC187777
0.5882	Remote Similarity	NPC174560
0.5882	Remote Similarity	NPC125312
0.5862	Remote Similarity	NPC604140
0.5769	Remote Similarity	NPC134782
0.5758	Remote Similarity	NPC18712
0.5758	Remote Similarity	NPC74845
0.5641	Remote Similarity	NPC274290
0.5625	Remote Similarity	NPC314679
0.5625	Remote Similarity	NPC117572
0.5625	Remote Similarity	NPC262968
0.561	Remote Similarity	NPC320642
0.561	Remote Similarity	NPC329550
0.5588	Remote Similarity	NPC87394
0.5588	Remote Similarity	NPC324004
0.5588	Remote Similarity	NPC328497
0.5588	Remote Similarity	NPC602547
0.5556	Remote Similarity	NPC40082
0.55	Remote Similarity	NPC323597
0.55	Remote Similarity	NPC211752
0.55	Remote Similarity	NPC318814
0.55	Remote Similarity	NPC320669
0.55	Remote Similarity	NPC323498
0.5476	Remote Similarity	NPC323045
0.5476	Remote Similarity	NPC49863
0.5476	Remote Similarity	NPC317881
0.5455	Remote Similarity	NPC129972
0.5455	Remote Similarity	NPC301528
0.5455	Remote Similarity	NPC71317
0.5455	Remote Similarity	NPC163746
0.5455	Remote Similarity	NPC103286
0.5385	Remote Similarity	NPC28205
0.5366	Remote Similarity	NPC317583
0.5349	Remote Similarity	NPC322461
0.5333	Remote Similarity	NPC202716
0.5312	Remote Similarity	NPC50457
0.5312	Remote Similarity	NPC604910
0.5238	Remote Similarity	NPC470320
0.5238	Remote Similarity	NPC235242
0.5227	Remote Similarity	NPC605544
0.5227	Remote Similarity	NPC607260
0.5143	Remote Similarity	NPC224227
0.5122	Remote Similarity	NPC99619
0.5116	Remote Similarity	NPC470410
0.5116	Remote Similarity	NPC470412
0.5111	Remote Similarity	NPC329249
0.5111	Remote Similarity	NPC92558

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC605284 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6711
0.1-0.2	2139
0.2-0.3	227
0.3-0.4	45
0.4-0.5	10
0.5-0.6	6
0.6-0.7	2
0.7-0.8	6
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9615	High Similarity	NPD3195	Phase 2
0.9615	High Similarity	NPD3196	Approved
0.8621	High Similarity	NPD4266	Phase 2
0.8	Intermediate Similarity	NPD3172	Approved
0.7667	Intermediate Similarity	NPD3173	Phase 4
0.7576	Intermediate Similarity	NPD3194	Phase 4
0.7308	Intermediate Similarity	NPD2270	Pre-clinical
0.7308	Intermediate Similarity	NPD633	Phase 3
0.7308	Intermediate Similarity	NPD9448	Phase 2
0.7143	Intermediate Similarity	NPD622	Pre-clinical
0.68	Remote Similarity	NPD9655	Phase 4
0.6579	Remote Similarity	NPD39	Phase 4
0.5625	Remote Similarity	NPD28	Approved
0.5625	Remote Similarity	NPD29	Phase 4
0.5625	Remote Similarity	NPD4222	Phase 3
0.5588	Remote Similarity	NPD3199	Clinical (unspecified phase)
0.5476	Remote Similarity	NPD4247	Clinical (unspecified phase)
0.5143	Remote Similarity	NPD3197	Phase 1

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