NPASS Compound

Natural Product: NPC600288

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 79 82 0 0 0 0 0 0 0 0999 V2000 4.2047 -1.1297 -2.2886 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1333 -0.2077 -1.7302 C 0 0 2 0 0 0 0 0 0 0 0 0 3.7840 0.5201 -0.5654 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9413 1.2726 -1.0930 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0046 1.3577 -2.3427 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0134 1.9220 -0.3589 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2039 1.6266 1.0776 C 0 0 2 0 0 0 0 0 0 0 0 0 6.4492 0.1389 1.3323 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3106 2.2523 2.0371 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7724 3.0978 2.8749 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9707 2.0028 2.1254 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9264 -0.9760 -1.4304 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0470 -2.0933 -0.4249 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5758 -2.4159 -0.0959 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2695 -3.7123 -0.4408 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2541 -1.3986 -0.8472 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6632 -1.8698 -2.2034 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4574 -0.9563 -0.1317 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8985 0.3074 -0.3442 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1641 1.1643 -1.2618 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6818 2.2085 -1.7017 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2204 0.8472 -1.7173 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7413 -0.2391 -0.8759 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8798 0.2171 0.5387 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1230 0.7704 0.3594 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6704 1.2729 1.7303 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7405 1.9589 -0.3227 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1206 2.2797 0.2230 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9737 1.0638 0.1190 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0200 1.1502 -0.5012 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4703 -0.1412 0.7808 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7911 -0.1641 2.2667 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2755 -1.3155 0.1935 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0509 -0.3918 0.4795 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4302 -1.3972 1.4435 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1658 -1.8268 0.7907 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7462 -2.9770 1.0790 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1578 -1.0594 -3.3934 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2181 -0.9081 -1.8952 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9268 -2.2058 -2.0773 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9514 0.5749 -2.4970 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9957 -0.0999 0.2986 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0723 1.3369 -0.2155 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0132 1.8140 -0.8627 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8322 3.0395 -0.4289 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2513 2.0705 1.3251 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4651 -0.4428 0.3928 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4008 -0.0607 1.8589 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6461 -0.1907 2.0365 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4474 1.9813 3.0055 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5641 -1.4755 -2.3651 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4703 -3.0066 -0.9149 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6271 -1.8489 0.4610 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4597 -2.2138 0.9883 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0858 -4.2718 -0.4239 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7129 -1.1237 -2.9899 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0365 -2.7165 -2.5889 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6987 -2.3181 -2.1382 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2229 0.6661 -2.8098 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8951 1.7418 -1.5646 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0027 -0.1150 1.1691 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7517 -0.1350 1.0841 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8429 1.3365 0.6340 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5116 1.5980 2.3557 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0724 2.2137 1.5401 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9776 0.5965 2.2393 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1402 2.8570 -0.1137 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8599 1.8370 -1.4112 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1064 2.5905 1.2781 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5157 3.1244 -0.3757 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1880 -0.8819 2.8188 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8622 -0.5035 2.3934 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7748 0.8664 2.6431 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1690 -2.1993 0.8500 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8003 -1.5821 -0.7833 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2942 -0.9531 0.0685 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0052 -0.9178 -0.5225 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1280 -2.2522 1.5889 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1928 -0.9820 2.4246 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 2 0 4 6 1 0 6 7 1 0 7 8 1 0 7 9 1 0 9 10 2 0 9 11 1 0 2 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 14 16 1 0 16 17 1 6 16 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 20 22 1 0 22 23 1 0 23 24 1 1 19 25 1 0 25 26 1 1 25 27 1 0 27 28 1 0 28 29 1 0 29 30 2 0 29 31 1 0 31 32 1 0 31 33 1 0 31 34 1 0 34 35 1 0 35 36 1 0 36 37 2 0 23 12 1 0 34 25 1 0 23 16 1 0 36 18 1 0 1 38 1 0 1 39 1 0 1 40 1 0 2 41 1 6 3 42 1 0 3 43 1 0 6 44 1 0 6 45 1 0 7 46 1 1 8 47 1 0 8 48 1 0 8 49 1 0 11 50 1 0 12 51 1 6 13 52 1 0 13 53 1 0 14 54 1 1 15 55 1 0 17 56 1 0 17 57 1 0 17 58 1 0 22 59 1 0 22 60 1 0 24 61 1 0 24 62 1 0 24 63 1 0 26 64 1 0 26 65 1 0 26 66 1 0 27 67 1 0 27 68 1 0 28 69 1 0 28 70 1 0 32 71 1 0 32 72 1 0 32 73 1 0 33 74 1 0 33 75 1 0 33 76 1 0 34 77 1 6 35 78 1 0 35 79 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 NPC600288 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	23633
0.1-0.2	24233
0.2-0.3	1745
0.3-0.4	158
0.4-0.5	46
0.5-0.6	23
0.6-0.7	9
0.7-0.8	0
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC241156
1.0	High Similarity	NPC488419
0.8571	High Similarity	NPC488423
0.803	Intermediate Similarity	NPC606047
0.791	Intermediate Similarity	NPC25750
0.791	Intermediate Similarity	NPC610087
0.7812	Intermediate Similarity	NPC488420
0.7812	Intermediate Similarity	NPC600686
0.7463	Intermediate Similarity	NPC488421
0.7188	Intermediate Similarity	NPC209882
0.7188	Intermediate Similarity	NPC607131
0.6944	Remote Similarity	NPC488422
0.6912	Remote Similarity	NPC125622
0.662	Remote Similarity	NPC243525
0.662	Remote Similarity	NPC40765
0.6479	Remote Similarity	NPC10364
0.6389	Remote Similarity	NPC55872
0.6301	Remote Similarity	NPC95565
0.6301	Remote Similarity	NPC609201
0.6286	Remote Similarity	NPC255809
0.56	Remote Similarity	NPC482586
0.5541	Remote Similarity	NPC107690
0.5526	Remote Similarity	NPC204450
0.5526	Remote Similarity	NPC205899
0.5526	Remote Similarity	NPC195290
0.5493	Remote Similarity	NPC11711
0.5455	Remote Similarity	NPC473038
0.5455	Remote Similarity	NPC16021
0.5395	Remote Similarity	NPC482588
0.5385	Remote Similarity	NPC604630
0.5375	Remote Similarity	NPC480124
0.5333	Remote Similarity	NPC607625
0.5325	Remote Similarity	NPC53222
0.5325	Remote Similarity	NPC482587
0.5309	Remote Similarity	NPC56498
0.5263	Remote Similarity	NPC482590
0.5263	Remote Similarity	NPC482589
0.519	Remote Similarity	NPC480125
0.5165	Remote Similarity	NPC600080
0.5132	Remote Similarity	NPC157787
0.5128	Remote Similarity	NPC51370
0.5109	Remote Similarity	NPC611554
0.5067	Remote Similarity	NPC18319

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC600288 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6346
0.1-0.2	2749
0.2-0.3	55
0.3-0.4	0
0.4-0.5	0
0.5-0.6	0
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
		NPD

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