NPASS Compound

Natural Product: NPC605821

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 50 49 0 0 0 0 0 0 0 0999 V2000 8.3018 0.1847 -0.4725 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2012 -0.6979 -1.0440 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1286 0.1498 -1.6712 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5147 1.0914 -0.6317 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9242 0.3005 0.4467 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6645 0.3092 0.7981 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6994 1.1420 0.1175 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3993 1.1455 0.4867 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4622 2.0001 -0.2267 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7946 2.0110 0.1215 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3463 1.2051 1.2067 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4306 0.2959 0.5199 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0351 -0.5534 1.5594 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0223 -1.5696 1.2438 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3209 -1.3291 0.6263 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3137 -0.8050 -0.7493 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7096 -0.6162 -1.3253 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5462 0.3238 -0.5922 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7365 0.4570 -0.9907 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1725 1.0899 0.4985 O 0 0 0 0 0 0 0 0 0 0 0 0 8.0544 0.3798 0.5880 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4972 1.0749 -1.0680 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2192 -0.4712 -0.4533 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8457 -1.3424 -0.2209 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6228 -1.3950 -1.8094 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5849 0.7258 -2.5015 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3316 -0.4597 -2.1061 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4111 1.6823 -0.2509 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8409 1.7867 -1.1507 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5870 -0.3519 1.0110 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3287 -0.3240 1.6220 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9670 1.7828 -0.6971 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1799 0.4945 1.2974 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8325 2.6349 -1.0629 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4900 2.6565 -0.4208 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6837 0.5856 1.7813 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9601 1.8848 1.8542 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8643 -0.2943 -0.2054 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0763 1.0790 0.0682 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1485 -1.1080 2.0466 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3883 0.0606 2.4512 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5202 -2.4045 0.6131 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1893 -2.1645 2.2222 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8657 -2.3422 0.6251 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9968 -0.7146 1.3102 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7308 0.1107 -0.8333 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8227 -1.5339 -1.4618 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2183 -1.5884 -1.4295 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5642 -0.2264 -2.3686 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6511 1.9723 0.6281 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 2 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 18 20 1 0 1 21 1 0 1 22 1 0 1 23 1 0 2 24 1 0 2 25 1 0 3 26 1 0 3 27 1 0 4 28 1 0 4 29 1 0 5 30 1 0 6 31 1 0 7 32 1 0 8 33 1 0 9 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 14 42 1 0 14 43 1 0 15 44 1 0 15 45 1 0 16 46 1 0 16 47 1 0 17 48 1 0 17 49 1 0 20 50 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 NPC605821 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	38558
0.1-0.2	9678
0.2-0.3	1237
0.3-0.4	209
0.4-0.5	61
0.5-0.6	41
0.6-0.7	49
0.7-0.8	1
0.8-0.85	9
0.85-0.9	1
0.9-0.95	3
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9286	High Similarity	NPC95145
0.9286	High Similarity	NPC325642
0.9286	High Similarity	NPC65174
0.8571	High Similarity	NPC281245
0.8276	Intermediate Similarity	NPC424
0.8276	Intermediate Similarity	NPC36061
0.8276	Intermediate Similarity	NPC69510
0.8276	Intermediate Similarity	NPC77272
0.8276	Intermediate Similarity	NPC290563
0.8276	Intermediate Similarity	NPC139029
0.8276	Intermediate Similarity	NPC281972
0.8276	Intermediate Similarity	NPC261831
0.8276	Intermediate Similarity	NPC87564
0.7667	Intermediate Similarity	NPC92114
0.75	Intermediate Similarity	NPC154245
0.75	Intermediate Similarity	NPC85813
0.75	Intermediate Similarity	NPC223697
0.75	Intermediate Similarity	NPC6095
0.7188	Intermediate Similarity	NPC321062
0.697	Remote Similarity	NPC52955
0.697	Remote Similarity	NPC88966
0.697	Remote Similarity	NPC25417
0.697	Remote Similarity	NPC1813
0.6842	Remote Similarity	NPC251042
0.6842	Remote Similarity	NPC255863
0.6842	Remote Similarity	NPC174447
0.6842	Remote Similarity	NPC136164
0.6842	Remote Similarity	NPC122521
0.6842	Remote Similarity	NPC245947
0.6786	Remote Similarity	NPC171736
0.6786	Remote Similarity	NPC301585
0.6786	Remote Similarity	NPC261080
0.6786	Remote Similarity	NPC132565
0.6786	Remote Similarity	NPC209970
0.6786	Remote Similarity	NPC216630
0.6786	Remote Similarity	NPC201844
0.6786	Remote Similarity	NPC301696
0.6786	Remote Similarity	NPC196924
0.6786	Remote Similarity	NPC307783
0.6786	Remote Similarity	NPC154186
0.6786	Remote Similarity	NPC149184
0.6786	Remote Similarity	NPC279026
0.6786	Remote Similarity	NPC113928
0.6786	Remote Similarity	NPC14227
0.6667	Remote Similarity	NPC180534
0.6667	Remote Similarity	NPC5413
0.6667	Remote Similarity	NPC318420
0.6667	Remote Similarity	NPC70387
0.6667	Remote Similarity	NPC326268
0.6667	Remote Similarity	NPC611531
0.6471	Remote Similarity	NPC59051
0.6429	Remote Similarity	NPC155263
0.6316	Remote Similarity	NPC106851
0.6316	Remote Similarity	NPC282788
0.6316	Remote Similarity	NPC274927
0.6316	Remote Similarity	NPC477201
0.6296	Remote Similarity	NPC214610
0.6296	Remote Similarity	NPC118968
0.6296	Remote Similarity	NPC183424
0.6296	Remote Similarity	NPC294085
0.625	Remote Similarity	NPC34416
0.6216	Remote Similarity	NPC225929
0.6216	Remote Similarity	NPC606120
0.6176	Remote Similarity	NPC91495
0.6154	Remote Similarity	NPC179764
0.6071	Remote Similarity	NPC175342
0.6061	Remote Similarity	NPC184171
0.6	Remote Similarity	NPC243532
0.5926	Remote Similarity	NPC268826
0.5882	Remote Similarity	NPC149821
0.5854	Remote Similarity	NPC68343
0.5854	Remote Similarity	NPC328089
0.5789	Remote Similarity	NPC487561
0.5625	Remote Similarity	NPC55023
0.5625	Remote Similarity	NPC21844
0.561	Remote Similarity	NPC187777
0.561	Remote Similarity	NPC473863
0.5588	Remote Similarity	NPC8219
0.5556	Remote Similarity	NPC174368
0.5556	Remote Similarity	NPC174560
0.5556	Remote Similarity	NPC125312
0.5484	Remote Similarity	NPC604140
0.5429	Remote Similarity	NPC18712
0.5429	Remote Similarity	NPC74845
0.5429	Remote Similarity	NPC207292
0.5366	Remote Similarity	NPC274290
0.5357	Remote Similarity	NPC134782
0.5349	Remote Similarity	NPC320642
0.5349	Remote Similarity	NPC329550
0.5294	Remote Similarity	NPC314679
0.5278	Remote Similarity	NPC87394
0.5278	Remote Similarity	NPC48162
0.5278	Remote Similarity	NPC324004
0.5278	Remote Similarity	NPC328497
0.5278	Remote Similarity	NPC602547
0.5263	Remote Similarity	NPC40082
0.5238	Remote Similarity	NPC318814
0.5238	Remote Similarity	NPC320669
0.5227	Remote Similarity	NPC323045
0.5227	Remote Similarity	NPC49863
0.5227	Remote Similarity	NPC317881
0.5217	Remote Similarity	NPC92558
0.5143	Remote Similarity	NPC129972
0.5143	Remote Similarity	NPC301528
0.5143	Remote Similarity	NPC71317
0.5143	Remote Similarity	NPC163746
0.5143	Remote Similarity	NPC103286
0.5122	Remote Similarity	NPC28205
0.5111	Remote Similarity	NPC322461

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC605821 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6817
0.1-0.2	2074
0.2-0.3	195
0.3-0.4	42
0.4-0.5	8
0.5-0.6	3
0.6-0.7	8
0.7-0.8	1
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8276	Intermediate Similarity	NPD3195	Phase 2
0.8276	Intermediate Similarity	NPD3196	Approved
0.75	Intermediate Similarity	NPD4266	Phase 2
0.697	Remote Similarity	NPD3172	Approved
0.6786	Remote Similarity	NPD2270	Pre-clinical
0.6786	Remote Similarity	NPD633	Phase 3
0.6786	Remote Similarity	NPD9448	Phase 2
0.6667	Remote Similarity	NPD3173	Phase 4
0.6667	Remote Similarity	NPD3194	Phase 4
0.6667	Remote Similarity	NPD622	Pre-clinical
0.6296	Remote Similarity	NPD9655	Phase 4
0.5854	Remote Similarity	NPD39	Phase 4
0.5278	Remote Similarity	NPD3199	Clinical (unspecified phase)
0.5227	Remote Similarity	NPD4247	Clinical (unspecified phase)

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