NPASS Compound

Natural Product: NPC582713

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 68 72 0 0 0 0 0 0 0 0999 V2000 -2.1300 -4.5229 2.5593 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0511 -3.1584 3.2397 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4978 -2.2007 2.1797 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4433 -2.2535 1.1282 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2347 -2.7735 1.6817 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5971 -1.7974 0.9985 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7185 -2.2952 0.3232 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9937 -3.6626 0.3183 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5805 -1.4769 -0.3506 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3162 -0.1258 -0.3510 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2311 0.7530 -1.0628 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9936 2.0018 -1.0668 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3895 0.2012 -1.7506 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2314 1.0719 -2.4103 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9364 2.4158 -2.3885 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6821 3.4237 -3.0025 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3519 0.5683 -3.0771 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6321 -0.7831 -3.0883 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7821 -1.6461 -2.4240 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6615 -1.1506 -1.7559 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7522 -2.0368 -1.0469 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9728 -3.2701 -1.0341 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2019 0.3676 0.3197 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0308 1.7567 0.2535 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3283 -0.4550 1.0018 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8300 0.1626 1.6920 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8053 0.6529 0.8678 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0328 1.9933 0.8960 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9936 2.6800 -0.4466 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3563 2.6462 -1.1100 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1769 3.6248 -0.4115 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.9513 1.2783 -0.7880 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1227 1.0907 -1.5151 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2185 1.2864 0.7136 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.6412 1.7210 0.9288 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3564 2.1702 1.3696 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4710 -0.7915 2.6685 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1312 -4.9865 2.4539 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5369 -4.4240 1.5204 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7900 -5.2157 3.0846 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0730 -2.8500 3.4675 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3825 -3.2239 4.1084 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0128 -2.4211 0.2612 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4278 -3.6939 1.0431 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2858 -3.2310 2.5809 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5222 -4.2057 -0.3938 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0755 4.3617 -3.0094 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0630 3.1354 -3.9821 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5589 3.6701 -2.3358 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9913 1.2650 -3.5827 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5108 -1.1647 -3.6135 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9820 -2.7179 -2.4184 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2057 2.3714 1.0177 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4161 1.0087 2.2708 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4024 2.5793 1.5880 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2845 2.2116 -1.1594 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6465 3.7490 -0.3365 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2986 2.8328 -2.1846 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6309 4.4684 -0.1332 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0340 3.8691 -0.9545 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1790 0.5149 -1.0211 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2602 0.1275 -1.6263 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1160 0.2504 1.1101 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7221 2.7590 1.3209 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1809 1.0746 1.6602 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2371 1.6852 -0.0247 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9804 -0.7864 3.6639 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5232 -0.4793 2.8430 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 6 3 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 7 9 1 0 9 10 2 0 10 11 1 0 11 12 2 0 11 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 14 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 2 0 10 23 1 0 23 24 1 0 23 25 2 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 30 32 1 0 32 33 1 0 32 34 1 0 34 35 1 0 34 36 1 0 26 37 1 0 37 3 1 0 25 6 1 0 36 28 1 0 21 9 1 0 20 13 1 0 1 38 1 0 1 39 1 0 1 40 1 0 2 41 1 0 2 42 1 0 4 43 1 0 5 44 1 0 5 45 1 0 8 46 1 0 16 47 1 0 16 48 1 0 16 49 1 0 17 50 1 0 18 51 1 0 19 52 1 0 24 53 1 0 26 54 1 1 28 55 1 1 29 56 1 0 29 57 1 0 30 58 1 6 31 59 1 0 31 60 1 0 32 61 1 1 33 62 1 0 34 63 1 1 35 64 1 0 35 65 1 0 35 66 1 0 37 67 1 0 37 68 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 NPC582713 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	11072
0.1-0.2	36707
0.2-0.3	2033
0.3-0.4	32
0.4-0.5	2
0.5-0.6	3
0.6-0.7	2
0.7-0.8	1
0.8-0.85	4
0.85-0.9	2
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC603200
0.8553	High Similarity	NPC601855
0.8533	High Similarity	NPC109403
0.8421	Intermediate Similarity	NPC487573
0.8205	Intermediate Similarity	NPC261012
0.8205	Intermediate Similarity	NPC314738
0.8101	Intermediate Similarity	NPC468994
0.7632	Intermediate Similarity	NPC602774
0.6883	Remote Similarity	NPC611971
0.6477	Remote Similarity	NPC600087
0.5444	Remote Similarity	NPC603758
0.5385	Remote Similarity	NPC487390
0.5158	Remote Similarity	NPC487386

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC582713 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	2881
0.1-0.2	6164
0.2-0.3	73
0.3-0.4	2
0.4-0.5	5
0.5-0.6	12
0.6-0.7	6
0.7-0.8	1
0.8-0.85	5
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8533	High Similarity	NPD6778	Phase 4
0.8421	Intermediate Similarity	NPD6777	Approved
0.8205	Intermediate Similarity	NPD6781	Phase 4
0.8205	Intermediate Similarity	NPD6782	Phase 4
0.8101	Intermediate Similarity	NPD6779	Approved
0.8101	Intermediate Similarity	NPD6780	Approved
0.7356	Intermediate Similarity	NPD6776	Approved
0.6977	Remote Similarity	NPD6823	Phase 2
0.6883	Remote Similarity	NPD6535	Phase 4
0.6795	Remote Similarity	NPD6534	Approved
0.6337	Remote Similarity	NPD8058	Clinical (unspecified phase)
0.6337	Remote Similarity	NPD8059	Phase 3
0.6	Remote Similarity	NPD7871	Phase 2
0.596	Remote Similarity	NPD7801	Approved
0.5938	Remote Similarity	NPD7696	Phase 3
0.5938	Remote Similarity	NPD7697	Phase 3
0.5938	Remote Similarity	NPD7698	Approved
0.5938	Remote Similarity	NPD7870	Phase 2
0.5922	Remote Similarity	NPD8155	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD7699	Phase 2
0.5714	Remote Similarity	NPD7700	Phase 2
0.5437	Remote Similarity	NPD7701	Phase 2
0.54	Remote Similarity	NPD7435	Phase 2
0.5283	Remote Similarity	NPD7874	Phase 4
0.5283	Remote Similarity	NPD7875	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