NPASS Compound

Natural Product: NPC609452

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 84 88 0 0 0 0 0 0 0 0999 V2000 3.8499 2.5108 0.2430 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5615 1.1741 0.4960 C 0 0 2 0 0 0 0 0 0 0 0 0 5.6694 1.5441 1.5028 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9934 2.0540 2.6193 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2800 0.7789 -0.7513 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3041 0.2248 -1.7248 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6566 -0.9927 -1.1787 C 0 0 2 0 0 0 0 0 0 0 0 0 4.6741 -2.0795 -1.2299 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7917 -1.8676 -1.7210 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4139 -3.3513 -0.7375 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6144 -1.4352 -2.1951 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3608 -0.6705 -2.2163 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7617 -0.3456 -0.8913 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6354 1.1343 -0.7778 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5927 -0.8464 0.2462 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0280 -1.2879 1.3853 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4173 -1.3390 1.6611 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1287 -0.6297 0.5769 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6372 -0.6164 0.7224 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.2088 -1.9765 0.5244 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9144 -0.2127 2.1559 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3577 0.1373 2.3215 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.5593 0.5787 3.6280 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7050 1.2492 1.3942 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0508 1.5617 1.5633 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4563 0.9525 -0.0618 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.6042 0.1738 -0.5991 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5070 2.3269 -0.7555 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5007 3.0966 -0.1750 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1016 0.4042 -0.2676 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8370 -0.1247 -1.6368 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4469 -0.5401 -1.9138 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6270 -1.0090 -0.7737 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3120 -2.5031 -0.8846 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0878 -0.8845 0.1962 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6703 0.1642 1.0871 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6213 2.5305 -0.8411 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5175 3.3748 0.4402 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9168 2.5434 0.8069 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2872 0.6815 1.7465 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2303 2.3951 1.0471 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8776 3.0354 2.5467 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0943 0.0759 -0.5581 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6903 1.7168 -1.2009 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6133 0.9715 -2.1512 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9126 -0.1169 -2.6179 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2025 -3.8608 -0.3590 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1227 -1.2891 -3.1961 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5226 -2.5344 -2.1062 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5243 0.2567 -2.8431 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6243 -1.2619 -2.8256 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8378 1.4844 0.2776 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4603 1.6505 -1.3597 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2788 1.5879 -1.1381 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6769 -1.6505 2.2046 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7860 -2.3575 1.8853 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5999 -0.7597 2.6159 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8602 0.4674 0.7060 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2739 -2.0232 0.8464 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6951 -2.6614 1.2524 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1950 -2.3604 -0.4964 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3010 0.6156 2.5032 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7328 -1.1401 2.7717 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0617 -0.6948 2.1664 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6554 -0.2380 4.1948 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0840 2.1326 1.6661 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3993 1.2935 2.4417 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4629 -0.2717 -1.5881 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0320 -0.5646 0.1364 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4589 0.9055 -0.7329 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3066 2.2625 -1.8289 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4643 2.8371 -0.5166 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8450 3.7940 0.4309 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4084 1.2932 -0.1404 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1146 0.7037 -2.3558 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5710 -0.9417 -1.9051 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5034 -1.3935 -2.6596 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9185 0.2535 -2.5251 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7229 -2.7390 -0.5686 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9585 -3.1474 -0.3045 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3914 -2.7973 -1.9550 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3417 -1.8738 0.7011 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8056 0.7277 1.5529 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1819 -0.2660 2.0010 H 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 2 3 1 0 3 4 1 0 2 5 1 0 5 6 1 0 6 7 1 0 7 8 1 1 8 9 2 0 8 10 1 0 7 11 1 0 11 12 1 0 12 13 1 0 13 14 1 1 13 15 1 0 15 16 2 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 6 19 21 1 0 21 22 1 0 22 23 1 0 22 24 1 0 24 25 1 0 24 26 1 0 26 27 1 6 26 28 1 0 28 29 1 0 26 30 1 0 30 31 1 0 31 32 1 0 32 33 1 0 33 34 1 1 15 35 1 0 35 36 1 0 36 2 1 0 35 7 1 0 33 13 1 0 33 18 1 0 30 19 1 0 1 37 1 0 1 38 1 0 1 39 1 0 3 40 1 0 3 41 1 0 4 42 1 0 5 43 1 0 5 44 1 0 6 45 1 0 6 46 1 0 10 47 1 0 11 48 1 0 11 49 1 0 12 50 1 0 12 51 1 0 14 52 1 0 14 53 1 0 14 54 1 0 16 55 1 0 17 56 1 0 17 57 1 0 18 58 1 1 20 59 1 0 20 60 1 0 20 61 1 0 21 62 1 0 21 63 1 0 22 64 1 6 23 65 1 0 24 66 1 1 25 67 1 0 27 68 1 0 27 69 1 0 27 70 1 0 28 71 1 0 28 72 1 0 29 73 1 0 30 74 1 1 31 75 1 0 31 76 1 0 32 77 1 0 32 78 1 0 34 79 1 0 34 80 1 0 34 81 1 0 35 82 1 1 36 83 1 0 36 84 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 NPC609452 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	23262
0.1-0.2	23186
0.2-0.3	2727
0.3-0.4	372
0.4-0.5	186
0.5-0.6	68
0.6-0.7	30
0.7-0.8	0
0.8-0.85	1
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8689	High Similarity	NPC231063
0.8689	High Similarity	NPC282395
0.8689	High Similarity	NPC472149
0.8387	Intermediate Similarity	NPC88116
0.7656	Intermediate Similarity	NPC121798
0.7656	Intermediate Similarity	NPC234346
0.7538	Intermediate Similarity	NPC173744
0.7538	Intermediate Similarity	NPC204961
0.7538	Intermediate Similarity	NPC73004
0.7538	Intermediate Similarity	NPC110308
0.7424	Intermediate Similarity	NPC32407
0.7424	Intermediate Similarity	NPC263548
0.7424	Intermediate Similarity	NPC606320
0.7385	Intermediate Similarity	NPC84319
0.7385	Intermediate Similarity	NPC52021
0.7385	Intermediate Similarity	NPC599947
0.7313	Intermediate Similarity	NPC247139
0.7121	Intermediate Similarity	NPC182797
0.7121	Intermediate Similarity	NPC52169
0.7121	Intermediate Similarity	NPC488562
0.7101	Intermediate Similarity	NPC20235
0.7101	Intermediate Similarity	NPC299996
0.7059	Intermediate Similarity	NPC201657
0.6912	Remote Similarity	NPC145667
0.6866	Remote Similarity	NPC307282
0.6761	Remote Similarity	NPC479743
0.6618	Remote Similarity	NPC270768
0.6618	Remote Similarity	NPC59263
0.6618	Remote Similarity	NPC210106
0.6571	Remote Similarity	NPC88847
0.6522	Remote Similarity	NPC106112
0.6522	Remote Similarity	NPC261935
0.6522	Remote Similarity	NPC37221
0.6522	Remote Similarity	NPC481314
0.6486	Remote Similarity	NPC188833
0.6479	Remote Similarity	NPC481316
0.6286	Remote Similarity	NPC71074
0.6286	Remote Similarity	NPC481360
0.6286	Remote Similarity	NPC605937
0.6197	Remote Similarity	NPC259733
0.6197	Remote Similarity	NPC158371
0.6197	Remote Similarity	NPC207922
0.6164	Remote Similarity	NPC324063
0.6143	Remote Similarity	NPC282616
0.6111	Remote Similarity	NPC9613
0.6081	Remote Similarity	NPC481315
0.6027	Remote Similarity	NPC25299
0.6027	Remote Similarity	NPC481322
0.6027	Remote Similarity	NPC130520
0.6	Remote Similarity	NPC480946
0.6	Remote Similarity	NPC130577
0.6	Remote Similarity	NPC142415
0.6	Remote Similarity	NPC102683
0.5972	Remote Similarity	NPC305464
0.5972	Remote Similarity	NPC19376
0.5972	Remote Similarity	NPC25848
0.5972	Remote Similarity	NPC298554
0.5867	Remote Similarity	NPC6255
0.5833	Remote Similarity	NPC158141
0.5753	Remote Similarity	NPC40092
0.5735	Remote Similarity	NPC478657
0.5733	Remote Similarity	NPC116457
0.5694	Remote Similarity	NPC275809
0.5694	Remote Similarity	NPC229281
0.5694	Remote Similarity	NPC306541
0.5694	Remote Similarity	NPC32118
0.5676	Remote Similarity	NPC191412
0.5676	Remote Similarity	NPC114159
0.5676	Remote Similarity	NPC6818
0.5652	Remote Similarity	NPC604575
0.5641	Remote Similarity	NPC96693
0.5616	Remote Similarity	NPC61543
0.5616	Remote Similarity	NPC271614
0.5616	Remote Similarity	NPC293048
0.5616	Remote Similarity	NPC225585
0.5616	Remote Similarity	NPC130278
0.5616	Remote Similarity	NPC111214
0.56	Remote Similarity	NPC607666
0.56	Remote Similarity	NPC608261
0.56	Remote Similarity	NPC611078
0.5556	Remote Similarity	NPC474806
0.5556	Remote Similarity	NPC133579
0.5526	Remote Similarity	NPC117663
0.5526	Remote Similarity	NPC481318
0.5479	Remote Similarity	NPC37038
0.5467	Remote Similarity	NPC35239
0.5417	Remote Similarity	NPC43686
0.5395	Remote Similarity	NPC127689
0.5333	Remote Similarity	NPC87095
0.5333	Remote Similarity	NPC136697
0.5325	Remote Similarity	NPC174663
0.5316	Remote Similarity	NPC481320
0.5278	Remote Similarity	NPC280654
0.527	Remote Similarity	NPC64872
0.527	Remote Similarity	NPC25906
0.5263	Remote Similarity	NPC132824
0.525	Remote Similarity	NPC481319
0.5195	Remote Similarity	NPC62516
0.519	Remote Similarity	NPC474727
0.5165	Remote Similarity	NPC488214
0.5135	Remote Similarity	NPC96916
0.5135	Remote Similarity	NPC187722
0.5135	Remote Similarity	NPC198664
0.5132	Remote Similarity	NPC202728
0.5132	Remote Similarity	NPC158059
0.5132	Remote Similarity	NPC291028
0.5132	Remote Similarity	NPC200752
0.5132	Remote Similarity	NPC120840
0.5128	Remote Similarity	NPC187933
0.5128	Remote Similarity	NPC600832
0.5119	Remote Similarity	NPC204407
0.5067	Remote Similarity	NPC51700
0.5067	Remote Similarity	NPC88716
0.5067	Remote Similarity	NPC156981
0.5067	Remote Similarity	NPC68160
0.5067	Remote Similarity	NPC606443
0.5065	Remote Similarity	NPC263393
0.5065	Remote Similarity	NPC474963
0.5059	Remote Similarity	NPC28198
0.5059	Remote Similarity	NPC476123
0.5059	Remote Similarity	NPC606107

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC609452 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6287
0.1-0.2	2815
0.2-0.3	44
0.3-0.4	4
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