NPASS Compound

Natural Product: NPC521431

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 55 58 0 0 0 0 0 0 0 0999 V2000 -2.3427 4.9315 0.4949 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8125 3.5301 0.5091 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7884 3.0812 1.5246 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3628 2.6769 -0.3835 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7758 1.2528 -0.4479 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6224 0.3321 -0.2841 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3304 0.7803 -0.0950 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7363 -0.0885 0.0565 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1254 0.3991 0.2598 C 0 0 1 0 0 0 0 0 0 0 0 0 2.6022 0.1551 1.6871 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9715 0.6674 1.7905 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3869 1.3351 2.7752 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9048 0.3946 0.7039 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2623 0.6333 0.8460 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1143 0.3634 -0.2025 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6100 -0.1417 -1.3844 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4858 -0.4146 -2.4502 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2605 -0.3757 -1.5166 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3819 -0.1096 -0.4685 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0362 -0.3326 -0.5725 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4453 -1.4361 0.0093 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8444 -1.9179 -0.1796 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8816 -1.0220 -0.3267 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1744 -1.4773 -0.5159 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5226 -2.8291 -0.5713 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5835 -3.1633 0.4681 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1177 -3.0975 -1.9384 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3699 -3.7441 -0.4075 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1277 -3.3452 -0.2259 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2248 5.5722 0.7259 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4969 5.0996 1.1939 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0314 5.2369 -0.5402 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0483 3.8511 2.2560 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3876 2.2043 2.1058 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7593 2.7577 1.0509 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6494 3.0139 -1.1223 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5016 0.9967 0.3531 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2342 1.0542 -1.4185 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1404 1.8256 -0.0636 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1956 1.4692 0.0691 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9293 0.6435 2.4253 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5440 -0.9533 1.8863 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5980 1.0284 1.7923 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1834 0.5468 -0.1032 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4765 -0.5270 -2.2887 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8724 -0.7688 -2.4380 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2557 -2.1489 0.1242 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2473 -2.9114 1.4891 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8463 -4.2360 0.3693 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4946 -2.5513 0.2612 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9973 -4.1707 -2.1904 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5908 -2.4351 -2.6539 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1846 -2.8052 -1.8867 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5760 -4.8013 -0.4413 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3105 -4.0287 -0.1099 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 2 3 4 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 11 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 16 18 1 0 18 19 2 0 19 20 1 0 8 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 24 25 1 0 25 26 1 0 25 27 1 0 25 28 1 0 28 29 2 0 23 6 1 0 20 9 1 0 29 22 1 0 19 13 1 0 1 30 1 0 1 31 1 0 1 32 1 0 3 33 1 0 3 34 1 0 3 35 1 0 4 36 1 0 5 37 1 0 5 38 1 0 7 39 1 0 9 40 1 6 10 41 1 0 10 42 1 0 14 43 1 0 15 44 1 0 17 45 1 0 18 46 1 0 21 47 1 0 26 48 1 0 26 49 1 0 26 50 1 0 27 51 1 0 27 52 1 0 27 53 1 0 28 54 1 0 29 55 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 NPC521431 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	19881
0.1-0.2	25920
0.2-0.3	3361
0.3-0.4	545
0.4-0.5	108
0.5-0.6	31
0.6-0.7	4
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC110303
1.0	High Similarity	NPC601247
0.7639	Intermediate Similarity	NPC132592
0.75	Intermediate Similarity	NPC209040
0.75	Intermediate Similarity	NPC111786
0.7424	Intermediate Similarity	NPC68104
0.7101	Intermediate Similarity	NPC23728
0.6716	Remote Similarity	NPC143896
0.6522	Remote Similarity	NPC221432
0.6522	Remote Similarity	NPC257097
0.6154	Remote Similarity	NPC101793
0.5949	Remote Similarity	NPC609256
0.5867	Remote Similarity	NPC291508
0.575	Remote Similarity	NPC160821
0.5714	Remote Similarity	NPC39752
0.5694	Remote Similarity	NPC39329
0.5694	Remote Similarity	NPC51032
0.5625	Remote Similarity	NPC227579
0.5625	Remote Similarity	NPC214166
0.56	Remote Similarity	NPC474033
0.5556	Remote Similarity	NPC169591
0.5556	Remote Similarity	NPC298223
0.5556	Remote Similarity	NPC604412
0.5538	Remote Similarity	NPC329225
0.5538	Remote Similarity	NPC147686
0.5513	Remote Similarity	NPC246948
0.5513	Remote Similarity	NPC142405
0.55	Remote Similarity	NPC477958
0.5441	Remote Similarity	NPC1612
0.5441	Remote Similarity	NPC183959
0.5333	Remote Similarity	NPC17170
0.5309	Remote Similarity	NPC40033
0.5294	Remote Similarity	NPC264083
0.5256	Remote Similarity	NPC312973
0.525	Remote Similarity	NPC474021
0.5244	Remote Similarity	NPC233980
0.5244	Remote Similarity	NPC481772
0.5244	Remote Similarity	NPC197679
0.5147	Remote Similarity	NPC476480
0.5147	Remote Similarity	NPC84585
0.5135	Remote Similarity	NPC164980
0.5059	Remote Similarity	NPC43319

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC521431 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3288
0.1-0.2	5781
0.2-0.3	73
0.3-0.4	6
0.4-0.5	1
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
0.5538	Remote Similarity	NPD1549	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