NPASS Compound

Natural Product: NPC599824

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 80 84 0 0 0 0 0 0 0 0999 V2000 -5.6302 0.9481 0.4505 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8197 -0.1409 1.0368 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0830 -0.1313 2.5554 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2978 -1.4660 0.4992 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0573 -1.3009 -0.6841 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2281 -2.4845 0.3699 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9929 -2.1067 -0.3338 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7776 -0.5771 -0.4066 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3835 -0.1562 -1.6774 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2765 -0.4231 -0.3085 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5648 -1.1010 -1.3920 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1011 -1.6274 -2.4024 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8843 -1.1420 -1.2382 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4854 -0.1541 -0.6375 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9558 -0.2496 -0.5090 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4596 -0.7997 0.7580 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9438 -1.1521 0.5813 C 0 0 1 0 0 0 0 0 0 0 0 0 5.6742 -0.9458 1.9196 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1450 -2.5286 0.1445 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8006 -3.3314 0.8425 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6164 -2.9755 -1.0490 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5717 -0.1354 -0.3516 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8575 1.2124 -0.2418 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5435 1.0228 -1.0193 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0298 0.8055 -2.4705 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7312 2.2425 -1.0166 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2386 2.1225 -1.0950 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7308 0.9996 -0.1443 C 0 0 2 0 0 0 0 0 0 0 0 0 1.2406 1.5383 1.1891 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7337 0.9219 -0.0521 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3171 2.0340 -0.8841 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2571 1.2127 1.3793 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7873 1.2596 1.3317 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3466 -0.0478 0.8717 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.2431 0.6164 -0.4406 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0758 1.8647 0.1751 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4269 1.3133 1.1688 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0053 0.8885 2.9598 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1314 -0.4619 2.7066 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4385 -0.8653 3.0721 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0552 -1.8924 1.2259 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8494 -2.0481 -1.2802 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6854 -3.3731 -0.1555 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0157 -2.8794 1.4069 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9959 -2.5194 -1.3771 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1376 -2.6141 0.1672 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8486 -0.9998 -2.2812 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5632 0.1676 -2.3809 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1754 0.5978 -1.6467 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0651 -1.0322 0.6353 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4550 -2.0179 -1.6449 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3268 -1.0534 -1.2361 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9700 -1.8014 0.8915 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3806 -0.2802 1.6819 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2383 -0.0169 2.3680 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5722 -1.8223 2.5732 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7371 -0.7129 1.7016 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6231 -3.9418 -1.3320 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6553 0.0170 -0.0721 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5736 -0.5507 -1.3557 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6554 1.3740 0.8133 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5056 1.9534 -0.7138 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9851 1.3204 -2.6458 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2930 1.3066 -3.1648 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0945 -0.2563 -2.7199 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9829 2.8666 -1.9379 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0956 2.9415 -0.2167 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0170 1.7455 -2.1129 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8200 3.0954 -0.8422 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9126 0.9680 2.0541 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8554 2.6060 1.1988 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3317 1.7467 1.1806 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9214 2.1548 -1.8802 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0984 2.9867 -0.3138 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4162 2.0403 -0.9557 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9980 0.3322 1.9723 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9895 2.1827 1.7612 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1914 2.1598 0.8945 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0683 1.3295 2.4305 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9393 -0.7787 1.6514 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 1 0 4 6 1 0 6 7 1 0 7 8 1 0 8 9 1 6 8 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 1 0 16 17 1 0 17 18 1 1 17 19 1 0 19 20 2 0 19 21 1 0 17 22 1 0 22 23 1 0 23 24 1 0 24 25 1 6 24 26 1 0 26 27 1 0 27 28 1 0 28 29 1 1 28 30 1 0 30 31 1 6 30 32 1 0 32 33 1 0 33 34 1 0 34 2 1 0 34 8 1 0 30 10 1 0 28 14 1 0 24 15 1 0 1 35 1 0 1 36 1 0 1 37 1 0 3 38 1 0 3 39 1 0 3 40 1 0 4 41 1 1 5 42 1 0 6 43 1 0 6 44 1 0 7 45 1 0 7 46 1 0 9 47 1 0 9 48 1 0 9 49 1 0 10 50 1 1 13 51 1 0 15 52 1 6 16 53 1 0 16 54 1 0 18 55 1 0 18 56 1 0 18 57 1 0 21 58 1 0 22 59 1 0 22 60 1 0 23 61 1 0 23 62 1 0 25 63 1 0 25 64 1 0 25 65 1 0 26 66 1 0 26 67 1 0 27 68 1 0 27 69 1 0 29 70 1 0 29 71 1 0 29 72 1 0 31 73 1 0 31 74 1 0 31 75 1 0 32 76 1 0 32 77 1 0 33 78 1 0 33 79 1 0 34 80 1 1 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 NPC599824 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	18029
0.1-0.2	26454
0.2-0.3	4476
0.3-0.4	709
0.4-0.5	131
0.5-0.6	33
0.6-0.7	13
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	5

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC4036
1.0	High Similarity	NPC65120
1.0	High Similarity	NPC145067
1.0	High Similarity	NPC233455
1.0	High Similarity	NPC158030
0.7424	Intermediate Similarity	NPC96095
0.7164	Intermediate Similarity	NPC171203
0.7164	Intermediate Similarity	NPC307426
0.7164	Intermediate Similarity	NPC98442
0.7164	Intermediate Similarity	NPC242468
0.7143	Intermediate Similarity	NPC482712
0.7143	Intermediate Similarity	NPC74751
0.675	Remote Similarity	NPC471967
0.662	Remote Similarity	NPC610635
0.6585	Remote Similarity	NPC482752
0.6522	Remote Similarity	NPC295643
0.6418	Remote Similarity	NPC602872
0.6389	Remote Similarity	NPC482711
0.6164	Remote Similarity	NPC263393
0.6056	Remote Similarity	NPC214756
0.6	Remote Similarity	NPC482747
0.6	Remote Similarity	NPC202666
0.6	Remote Similarity	NPC471961
0.6	Remote Similarity	NPC482746
0.6	Remote Similarity	NPC242015
0.5946	Remote Similarity	NPC281524
0.5946	Remote Similarity	NPC474525
0.5934	Remote Similarity	NPC482741
0.5934	Remote Similarity	NPC482745
0.5934	Remote Similarity	NPC482743
0.5934	Remote Similarity	NPC146753
0.5915	Remote Similarity	NPC95246
0.587	Remote Similarity	NPC471965
0.587	Remote Similarity	NPC482749
0.5867	Remote Similarity	NPC474529
0.5806	Remote Similarity	NPC14617
0.5694	Remote Similarity	NPC479748
0.5658	Remote Similarity	NPC46441
0.5625	Remote Similarity	NPC262199
0.5616	Remote Similarity	NPC272075
0.56	Remote Similarity	NPC155120
0.56	Remote Similarity	NPC288833
0.5584	Remote Similarity	NPC471966
0.5541	Remote Similarity	NPC7260
0.5541	Remote Similarity	NPC210037
0.5541	Remote Similarity	NPC263272
0.5541	Remote Similarity	NPC120968
0.5541	Remote Similarity	NPC227467
0.5541	Remote Similarity	NPC273621
0.5395	Remote Similarity	NPC98874
0.5395	Remote Similarity	NPC148523
0.5385	Remote Similarity	NPC198818
0.525	Remote Similarity	NPC169343
0.5128	Remote Similarity	NPC474964
0.5067	Remote Similarity	NPC477872
0.5065	Remote Similarity	NPC474537
0.5063	Remote Similarity	NPC476064
0.5059	Remote Similarity	NPC476878

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC599824 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5742
0.1-0.2	3289
0.2-0.3	109
0.3-0.4	2
0.4-0.5	2
0.5-0.6	2
0.6-0.7	2
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD7515	Phase 2
0.7143	Intermediate Similarity	NPD7748	Pre-clinical
0.6667	Remote Similarity	NPD7902	Phase 4
0.6	Remote Similarity	NPD8328	Phase 2
0.5122	Remote Similarity	NPD7900	Approved
0.5122	Remote Similarity	NPD7901	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