NPASS Compound

Natural Product: NPC603284

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 35 37 0 0 0 0 0 0 0 0999 V2000 -2.2670 2.4251 0.8500 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5715 0.9802 0.6336 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8751 0.5298 0.7746 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8806 1.4240 1.1144 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1814 -0.8129 0.5775 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1771 -1.6848 0.2419 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4265 -3.0455 0.0317 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9010 -1.2177 0.1088 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5478 0.1035 0.2938 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2274 0.5465 0.1485 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7679 -0.4451 0.3124 C 0 0 2 0 0 0 0 0 0 0 0 0 2.1263 0.0545 0.0432 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4412 0.8424 -1.0478 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7350 1.2930 -1.2654 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7629 0.9747 -0.4031 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0676 1.4172 -0.6045 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4550 0.1887 0.6876 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1654 -0.2565 0.8984 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4635 -1.5676 -0.6568 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8391 -2.1532 -0.2485 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9557 -3.3861 -0.2324 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4823 2.9844 -0.0814 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2243 2.5966 1.1669 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9638 2.7981 1.6147 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8221 1.2432 0.8010 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1817 -1.2046 0.6771 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2102 -3.5168 -0.8371 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7138 -0.7798 1.3669 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6274 1.0887 -1.7216 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9469 1.9044 -2.1239 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6502 1.0076 -1.3498 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2799 -0.0570 1.3645 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9377 -0.8813 1.7717 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3404 -1.0774 -1.6634 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2538 -2.3163 -0.7273 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 3 5 1 0 5 6 2 0 6 7 1 0 6 8 1 0 8 9 2 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 15 17 1 0 17 18 2 0 11 19 1 0 19 20 1 0 20 21 2 0 9 2 1 0 18 12 1 0 20 8 1 0 1 22 1 0 1 23 1 0 1 24 1 0 4 25 1 0 5 26 1 0 7 27 1 0 11 28 1 1 13 29 1 0 14 30 1 0 16 31 1 0 17 32 1 0 18 33 1 0 19 34 1 0 19 35 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 NPC603284 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	25706
0.1-0.2	19809
0.2-0.3	3573
0.3-0.4	489
0.4-0.5	201
0.5-0.6	59
0.6-0.7	11
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8	Intermediate Similarity	NPC213322
0.7292	Intermediate Similarity	NPC167624
0.7292	Intermediate Similarity	NPC166482
0.6981	Remote Similarity	NPC480991
0.6939	Remote Similarity	NPC4743
0.6852	Remote Similarity	NPC107572
0.6852	Remote Similarity	NPC32739
0.6735	Remote Similarity	NPC32441
0.6735	Remote Similarity	NPC79943
0.6667	Remote Similarity	NPC485881
0.64	Remote Similarity	NPC482121
0.64	Remote Similarity	NPC270964
0.6154	Remote Similarity	NPC324386
0.6066	Remote Similarity	NPC69531
0.5968	Remote Similarity	NPC166934
0.5849	Remote Similarity	NPC329203
0.5849	Remote Similarity	NPC222342
0.5769	Remote Similarity	NPC248372
0.5763	Remote Similarity	NPC470133
0.5763	Remote Similarity	NPC220998
0.5741	Remote Similarity	NPC469764
0.5741	Remote Similarity	NPC192083
0.5577	Remote Similarity	NPC225153
0.5577	Remote Similarity	NPC479876
0.5556	Remote Similarity	NPC300668
0.5556	Remote Similarity	NPC194432
0.5556	Remote Similarity	NPC296917
0.5556	Remote Similarity	NPC110776
0.5556	Remote Similarity	NPC170907
0.5517	Remote Similarity	NPC76372
0.5517	Remote Similarity	NPC37496
0.55	Remote Similarity	NPC66515
0.549	Remote Similarity	NPC106914
0.549	Remote Similarity	NPC329225
0.549	Remote Similarity	NPC86502
0.549	Remote Similarity	NPC147686
0.5472	Remote Similarity	NPC243083
0.5472	Remote Similarity	NPC13768
0.5472	Remote Similarity	NPC287246
0.5455	Remote Similarity	NPC321011
0.5455	Remote Similarity	NPC224851
0.5455	Remote Similarity	NPC294852
0.5455	Remote Similarity	NPC188679
0.5455	Remote Similarity	NPC475267
0.5455	Remote Similarity	NPC606248
0.5424	Remote Similarity	NPC324436
0.5424	Remote Similarity	NPC78
0.541	Remote Similarity	NPC134171
0.5333	Remote Similarity	NPC265040
0.5333	Remote Similarity	NPC148757
0.5273	Remote Similarity	NPC274784
0.5273	Remote Similarity	NPC20709
0.5273	Remote Similarity	NPC110038
0.5254	Remote Similarity	NPC164980
0.5231	Remote Similarity	NPC51760
0.5224	Remote Similarity	NPC479210
0.5211	Remote Similarity	NPC475184
0.5185	Remote Similarity	NPC295261
0.5185	Remote Similarity	NPC296490
0.5179	Remote Similarity	NPC324134
0.5179	Remote Similarity	NPC40833
0.5161	Remote Similarity	NPC76338
0.5161	Remote Similarity	NPC250242
0.5091	Remote Similarity	NPC20354
0.5091	Remote Similarity	NPC188022
0.5091	Remote Similarity	NPC177354
0.5088	Remote Similarity	NPC2416
0.5088	Remote Similarity	NPC271590
0.5085	Remote Similarity	NPC236637
0.5082	Remote Similarity	NPC477841
0.5077	Remote Similarity	NPC611447
0.5075	Remote Similarity	NPC475052
0.507	Remote Similarity	NPC479054

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC603284 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4392
0.1-0.2	4634
0.2-0.3	110
0.3-0.4	9
0.4-0.5	1
0.5-0.6	3
0.6-0.7	1
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
0.6735	Remote Similarity	NPD1552	Clinical (unspecified phase)
0.5741	Remote Similarity	NPD2393	Clinical (unspecified phase)
0.549	Remote Similarity	NPD1549	Phase 2
0.5472	Remote Similarity	NPD1550	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