NPASS Compound

Natural Product: NPC526302

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 62 65 0 0 0 0 0 0 0 0999 V2000 -2.1725 1.7938 -2.4337 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4836 0.8905 -1.4272 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5316 0.2523 -0.6790 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1976 0.5545 -0.9769 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8305 -0.0158 -0.3026 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2463 0.2733 -0.5828 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6000 1.1578 -1.5642 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9705 1.3736 -1.7636 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3316 2.1810 -2.6581 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9064 0.7160 -0.9966 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2675 0.9049 -1.1662 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7145 1.7854 -2.1402 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1918 0.2310 -0.3815 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5621 0.3975 -0.5256 O 0 0 0 0 0 0 0 0 0 0 0 0 9.1695 1.4301 0.2600 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7392 -0.6460 0.5883 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6712 -1.3165 1.3695 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1815 -2.2065 2.3527 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3671 -0.8294 0.7515 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4404 -0.1564 -0.0323 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1602 -0.3516 0.1467 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5027 -0.9237 0.7087 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8025 -1.2182 0.9988 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8768 -0.6293 0.3021 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1162 -0.9799 0.6573 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3758 -0.6406 0.2355 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1418 -0.0062 1.2189 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2950 0.5571 0.7529 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.2770 0.8948 1.8587 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7177 1.8000 2.7583 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9704 -0.2091 -0.3607 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.4437 0.2176 -1.5647 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6250 -1.6657 -0.1961 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.0622 -2.1961 0.9994 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1378 -1.8153 -0.3683 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.7975 -1.9537 -1.7054 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1167 2.1966 -2.8950 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6129 2.6602 -2.0275 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5767 1.2716 -3.2093 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0097 1.2672 -1.7728 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8711 1.6765 -2.1688 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5372 1.5477 -3.1018 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5008 1.7305 1.1079 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1244 1.1089 0.7008 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2686 2.3389 -0.3834 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0263 -2.6497 2.9347 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5070 -1.6483 3.0633 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6069 -3.0479 1.9263 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0333 -1.5254 1.5220 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3269 -1.3931 1.2629 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0029 -1.9322 1.7959 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3318 0.0927 -0.5860 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0140 1.5592 0.3118 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1534 1.4040 1.3972 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5855 0.0124 2.4409 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3499 2.5999 2.2752 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0587 -0.0177 -0.2732 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2447 1.1951 -1.5458 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1194 -2.2211 -1.0210 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2441 -2.3048 1.5799 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8268 -2.7348 0.1672 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3837 -2.8378 -1.8808 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 8 10 1 0 10 11 2 0 11 12 1 0 11 13 1 0 13 14 1 0 14 15 1 0 13 16 2 0 16 17 1 0 17 18 1 0 16 19 1 0 19 20 2 0 20 21 1 0 5 22 2 0 22 23 1 0 23 24 2 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 28 31 1 0 31 32 1 0 31 33 1 0 33 34 1 0 33 35 1 0 35 36 1 0 24 3 1 0 35 26 1 0 21 6 1 0 20 10 1 0 1 37 1 0 1 38 1 0 1 39 1 0 4 40 1 0 7 41 1 0 12 42 1 0 15 43 1 0 15 44 1 0 15 45 1 0 18 46 1 0 18 47 1 0 18 48 1 0 19 49 1 0 22 50 1 0 23 51 1 0 26 52 1 6 28 53 1 6 29 54 1 0 29 55 1 0 30 56 1 0 31 57 1 6 32 58 1 0 33 59 1 6 34 60 1 0 35 61 1 1 36 62 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 NPC526302 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	19281
0.1-0.2	26399
0.2-0.3	2820
0.3-0.4	943
0.4-0.5	295
0.5-0.6	66
0.6-0.7	28
0.7-0.8	0
0.8-0.85	3
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC609451
0.8592	High Similarity	NPC58053
0.8356	Intermediate Similarity	NPC186807
0.8158	Intermediate Similarity	NPC607707
0.8026	Intermediate Similarity	NPC605067
0.7973	Intermediate Similarity	NPC93337
0.7922	Intermediate Similarity	NPC602805
0.7867	Intermediate Similarity	NPC105025
0.7867	Intermediate Similarity	NPC45638
0.7792	Intermediate Similarity	NPC243930
0.7763	Intermediate Similarity	NPC201292
0.7692	Intermediate Similarity	NPC88023
0.725	Intermediate Similarity	NPC309025
0.6875	Remote Similarity	NPC182045
0.6835	Remote Similarity	NPC95090
0.6835	Remote Similarity	NPC27408
0.6812	Remote Similarity	NPC69394
0.6506	Remote Similarity	NPC22832
0.6506	Remote Similarity	NPC21666
0.6471	Remote Similarity	NPC211594
0.6463	Remote Similarity	NPC117260
0.6429	Remote Similarity	NPC311830
0.6341	Remote Similarity	NPC24043
0.6341	Remote Similarity	NPC603655
0.6296	Remote Similarity	NPC143851
0.6279	Remote Similarity	NPC172807
0.6207	Remote Similarity	NPC254540
0.619	Remote Similarity	NPC488071
0.6163	Remote Similarity	NPC488072
0.6118	Remote Similarity	NPC284960
0.6118	Remote Similarity	NPC601144
0.6111	Remote Similarity	NPC204693
0.6098	Remote Similarity	NPC261866
0.6098	Remote Similarity	NPC110349
0.6098	Remote Similarity	NPC39360
0.6098	Remote Similarity	NPC45618
0.6098	Remote Similarity	NPC29763
0.6098	Remote Similarity	NPC210003
0.6024	Remote Similarity	NPC146792
0.6024	Remote Similarity	NPC189142
0.6024	Remote Similarity	NPC77660
0.5952	Remote Similarity	NPC58716
0.5914	Remote Similarity	NPC483707
0.5833	Remote Similarity	NPC168822
0.5833	Remote Similarity	NPC145379
0.5814	Remote Similarity	NPC191306
0.5814	Remote Similarity	NPC224462
0.5775	Remote Similarity	NPC75279
0.5765	Remote Similarity	NPC610763
0.5747	Remote Similarity	NPC601710
0.5698	Remote Similarity	NPC205076
0.5682	Remote Similarity	NPC307518
0.5618	Remote Similarity	NPC48773
0.5604	Remote Similarity	NPC603300
0.56	Remote Similarity	NPC160951
0.5581	Remote Similarity	NPC181712
0.5568	Remote Similarity	NPC486578
0.5529	Remote Similarity	NPC289667
0.5526	Remote Similarity	NPC47781
0.5517	Remote Similarity	NPC222936
0.5479	Remote Similarity	NPC239128
0.5465	Remote Similarity	NPC259152
0.5417	Remote Similarity	NPC124155
0.5405	Remote Similarity	NPC120163
0.5405	Remote Similarity	NPC276409
0.5349	Remote Similarity	NPC83283
0.5333	Remote Similarity	NPC163780
0.5333	Remote Similarity	NPC25270
0.5326	Remote Similarity	NPC473682
0.5319	Remote Similarity	NPC607513
0.5281	Remote Similarity	NPC285197
0.5275	Remote Similarity	NPC601586
0.5263	Remote Similarity	NPC255350
0.5227	Remote Similarity	NPC84362
0.5227	Remote Similarity	NPC27640
0.5195	Remote Similarity	NPC283600
0.5195	Remote Similarity	NPC195202
0.5169	Remote Similarity	NPC472459
0.5169	Remote Similarity	NPC27942
0.5152	Remote Similarity	NPC475382
0.5114	Remote Similarity	NPC105511
0.5114	Remote Similarity	NPC64305
0.5114	Remote Similarity	NPC277205
0.5114	Remote Similarity	NPC37919
0.5114	Remote Similarity	NPC323593
0.5114	Remote Similarity	NPC203500
0.5109	Remote Similarity	NPC469931
0.5102	Remote Similarity	NPC150767
0.5065	Remote Similarity	NPC176300
0.5057	Remote Similarity	NPC473043
0.5057	Remote Similarity	NPC135345
0.5057	Remote Similarity	NPC331652
0.5056	Remote Similarity	NPC245014
0.5056	Remote Similarity	NPC84265
0.5056	Remote Similarity	NPC488080
0.5056	Remote Similarity	NPC169977
0.5056	Remote Similarity	NPC73511
0.5056	Remote Similarity	NPC602537
0.5055	Remote Similarity	NPC101026
0.5055	Remote Similarity	NPC148710
0.5055	Remote Similarity	NPC120099
0.5055	Remote Similarity	NPC80188
0.5055	Remote Similarity	NPC488077
0.5055	Remote Similarity	NPC609478
0.5052	Remote Similarity	NPC284277
0.5052	Remote Similarity	NPC475366
0.5052	Remote Similarity	NPC475497

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC526302 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5048
0.1-0.2	4000
0.2-0.3	85
0.3-0.4	10
0.4-0.5	6
0.5-0.6	1
0.6-0.7	0
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
0.5263	Remote Similarity	NPD2801	Pre-clinical

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