NPASS Compound

Natural Product: NPC599947

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 82 86 0 0 0 0 0 0 0 0999 V2000 -5.3033 0.2363 2.7489 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6816 -0.0941 1.3618 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9490 -1.5474 1.1964 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5526 0.6653 0.3876 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9766 0.4489 -0.9556 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6222 1.1108 -1.1366 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.0101 2.5372 -1.5165 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7041 3.0519 -2.6133 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7279 3.3297 -0.6444 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9814 0.5741 -2.3553 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5945 0.1141 -2.4200 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9227 -0.1450 -1.0583 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5762 -1.4613 -0.6652 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4222 1.0034 -0.2681 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5820 1.9462 0.0380 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8532 1.9526 -0.3568 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3048 0.5294 -0.1557 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7998 0.3989 -0.1460 C 0 0 1 0 0 0 0 0 0 0 0 0 3.5291 1.0012 -1.2802 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2520 1.2023 1.0989 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6871 0.9334 1.4467 C 0 0 1 0 0 0 0 0 0 0 0 0 4.8739 1.4966 2.7287 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1211 -0.4629 1.4854 C 0 0 1 0 0 0 0 0 0 0 0 0 4.9002 -1.0003 2.7656 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5358 -1.3694 0.4396 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4365 -1.4871 -0.7353 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5039 -2.7740 1.0823 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1284 -1.0000 0.2082 C 0 0 2 0 0 0 0 0 0 0 0 0 2.3949 -2.0245 -0.6320 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8980 -1.7746 -0.5893 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5358 -0.3609 -1.0844 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0191 -0.3267 -2.5059 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8271 1.1543 0.1318 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2640 0.3282 1.2874 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3884 -0.0157 2.6314 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1527 1.2884 2.9857 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8733 -0.4905 3.4422 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2212 -2.1250 1.8451 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8233 -1.9694 0.2000 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9486 -1.8158 1.6487 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6162 0.3344 0.4464 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5676 1.7102 0.7553 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7118 0.8944 -1.6908 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9146 -0.5994 -1.2273 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6462 4.3268 -0.5816 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6363 -0.2997 -2.7142 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1536 1.2748 -3.2566 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5607 -0.8387 -3.0320 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0073 0.8325 -3.0212 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2233 -1.9618 0.1962 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7075 -1.3526 -0.7131 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4326 -2.1285 -1.5663 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9221 2.8178 0.6297 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9538 2.2244 -1.4515 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4123 2.7114 0.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9929 0.2360 0.8689 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0604 0.3061 -1.9604 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8380 1.6763 -1.8367 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3496 1.7079 -0.9491 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5968 0.9780 1.9388 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2434 2.3092 0.8669 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3956 1.5133 0.7875 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9292 2.4851 2.6770 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2345 -0.5066 1.3464 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5828 -0.5715 3.3371 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2458 -2.2367 -0.4710 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0098 -1.8679 -1.6595 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0277 -0.5714 -0.9611 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4792 -3.5245 0.2774 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6772 -2.8824 1.7886 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5115 -2.8663 1.5715 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6318 -1.1360 1.2273 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8135 -2.2241 -1.6068 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5301 -2.9922 -0.0556 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4553 -2.5758 -1.1566 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6687 -1.7532 0.5068 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9990 0.6614 -2.9871 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4044 -1.0135 -3.1213 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0543 -0.7120 -2.6533 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9746 2.2174 0.5242 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1028 0.8875 2.2709 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5886 -0.5486 1.5159 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 5 6 1 0 6 7 1 6 7 8 2 0 7 9 1 0 6 10 1 0 10 11 1 0 11 12 1 0 12 13 1 1 12 14 1 0 14 15 2 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 6 18 20 1 0 20 21 1 0 21 22 1 0 21 23 1 0 23 24 1 0 23 25 1 0 25 26 1 0 25 27 1 0 25 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 1 6 14 33 1 0 33 34 1 0 34 2 1 0 33 6 1 0 31 12 1 0 31 17 1 0 28 18 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 0 4 42 1 0 5 43 1 0 5 44 1 0 9 45 1 0 10 46 1 0 10 47 1 0 11 48 1 0 11 49 1 0 13 50 1 0 13 51 1 0 13 52 1 0 15 53 1 0 16 54 1 0 16 55 1 0 17 56 1 0 19 57 1 0 19 58 1 0 19 59 1 0 20 60 1 0 20 61 1 0 21 62 1 6 22 63 1 0 23 64 1 6 24 65 1 0 26 66 1 0 26 67 1 0 26 68 1 0 27 69 1 0 27 70 1 0 27 71 1 0 28 72 1 1 29 73 1 0 29 74 1 0 30 75 1 0 30 76 1 0 32 77 1 0 32 78 1 0 32 79 1 0 33 80 1 0 34 81 1 0 34 82 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 NPC599947 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	25316
0.1-0.2	21102
0.2-0.3	2709
0.3-0.4	367
0.4-0.5	195
0.5-0.6	85
0.6-0.7	46
0.7-0.8	0
0.8-0.85	0
0.85-0.9	4
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC84319
1.0	High Similarity	NPC52021
0.8525	High Similarity	NPC231063
0.8525	High Similarity	NPC282395
0.8525	High Similarity	NPC472149
0.8525	High Similarity	NPC110308
0.7778	Intermediate Similarity	NPC306541
0.7619	Intermediate Similarity	NPC480946
0.7619	Intermediate Similarity	NPC130577
0.7619	Intermediate Similarity	NPC142415
0.7619	Intermediate Similarity	NPC102683
0.7385	Intermediate Similarity	NPC106112
0.7385	Intermediate Similarity	NPC261935
0.7385	Intermediate Similarity	NPC71074
0.7385	Intermediate Similarity	NPC37221
0.7385	Intermediate Similarity	NPC481360
0.7385	Intermediate Similarity	NPC605937
0.7385	Intermediate Similarity	NPC609452
0.7273	Intermediate Similarity	NPC259733
0.7273	Intermediate Similarity	NPC158371
0.7273	Intermediate Similarity	NPC207922
0.7231	Intermediate Similarity	NPC307282
0.7121	Intermediate Similarity	NPC88116
0.7059	Intermediate Similarity	NPC25299
0.7059	Intermediate Similarity	NPC481322
0.697	Remote Similarity	NPC270768
0.697	Remote Similarity	NPC59263
0.697	Remote Similarity	NPC210106
0.697	Remote Similarity	NPC282616
0.6912	Remote Similarity	NPC201657
0.6765	Remote Similarity	NPC145667
0.6765	Remote Similarity	NPC298554
0.6719	Remote Similarity	NPC604575
0.6716	Remote Similarity	NPC275809
0.6618	Remote Similarity	NPC158141
0.6575	Remote Similarity	NPC188833
0.6567	Remote Similarity	NPC474806
0.6567	Remote Similarity	NPC133579
0.6471	Remote Similarity	NPC182797
0.6471	Remote Similarity	NPC64872
0.6471	Remote Similarity	NPC37038
0.6471	Remote Similarity	NPC25906
0.6471	Remote Similarity	NPC32118
0.6471	Remote Similarity	NPC52169
0.6471	Remote Similarity	NPC488562
0.6377	Remote Similarity	NPC173744
0.6377	Remote Similarity	NPC204961
0.6377	Remote Similarity	NPC73004
0.6377	Remote Similarity	NPC481314
0.6338	Remote Similarity	NPC481316
0.6324	Remote Similarity	NPC198664
0.6301	Remote Similarity	NPC474727
0.6286	Remote Similarity	NPC228784
0.6286	Remote Similarity	NPC324341
0.6286	Remote Similarity	NPC32407
0.6286	Remote Similarity	NPC263548
0.6286	Remote Similarity	NPC601810
0.6286	Remote Similarity	NPC606320
0.6269	Remote Similarity	NPC280654
0.6197	Remote Similarity	NPC247139
0.6143	Remote Similarity	NPC271614
0.6143	Remote Similarity	NPC130278
0.6087	Remote Similarity	NPC96916
0.6056	Remote Similarity	NPC291028
0.6056	Remote Similarity	NPC200752
0.6056	Remote Similarity	NPC120840
0.6027	Remote Similarity	NPC20235
0.6027	Remote Similarity	NPC299996
0.6	Remote Similarity	NPC121798
0.6	Remote Similarity	NPC156981
0.6	Remote Similarity	NPC234346
0.5972	Remote Similarity	NPC474963
0.5946	Remote Similarity	NPC481315
0.5942	Remote Similarity	NPC43686
0.5942	Remote Similarity	NPC609710
0.593	Remote Similarity	NPC488214
0.5915	Remote Similarity	NPC300351
0.5811	Remote Similarity	NPC296164
0.5797	Remote Similarity	NPC49320
0.575	Remote Similarity	NPC204407
0.5733	Remote Similarity	NPC479743
0.5733	Remote Similarity	NPC96580
0.5714	Remote Similarity	NPC96693
0.5679	Remote Similarity	NPC283849
0.5679	Remote Similarity	NPC28198
0.5679	Remote Similarity	NPC476123
0.5679	Remote Similarity	NPC606107
0.5634	Remote Similarity	NPC187722
0.5634	Remote Similarity	NPC136313
0.5616	Remote Similarity	NPC202728
0.5616	Remote Similarity	NPC158059
0.5616	Remote Similarity	NPC87095
0.56	Remote Similarity	NPC222047
0.5581	Remote Similarity	NPC171007
0.5581	Remote Similarity	NPC190849
0.5556	Remote Similarity	NPC51700
0.5556	Remote Similarity	NPC88716
0.5556	Remote Similarity	NPC68160
0.5556	Remote Similarity	NPC606443
0.5542	Remote Similarity	NPC286347
0.5541	Remote Similarity	NPC91010
0.5479	Remote Similarity	NPC111214
0.5476	Remote Similarity	NPC100383
0.5467	Remote Similarity	NPC471588
0.5467	Remote Similarity	NPC130520
0.5465	Remote Similarity	NPC266365
0.5465	Remote Similarity	NPC191410
0.5405	Remote Similarity	NPC256247
0.5405	Remote Similarity	NPC305464
0.5405	Remote Similarity	NPC19376
0.5405	Remote Similarity	NPC293564
0.5405	Remote Similarity	NPC25848
0.5405	Remote Similarity	NPC29765
0.5395	Remote Similarity	NPC157113
0.5393	Remote Similarity	NPC605663
0.5385	Remote Similarity	NPC601365
0.5362	Remote Similarity	NPC478657
0.5349	Remote Similarity	NPC294112
0.5349	Remote Similarity	NPC284807
0.5333	Remote Similarity	NPC35239
0.5333	Remote Similarity	NPC88847
0.5333	Remote Similarity	NPC132126
0.5316	Remote Similarity	NPC481362
0.5301	Remote Similarity	NPC258130
0.5281	Remote Similarity	NPC198621
0.5281	Remote Similarity	NPC216940
0.5263	Remote Similarity	NPC62516
0.5227	Remote Similarity	NPC475472
0.52	Remote Similarity	NPC136697
0.52	Remote Similarity	NPC600164
0.5195	Remote Similarity	NPC324063
0.5195	Remote Similarity	NPC116457
0.5195	Remote Similarity	NPC174663
0.5195	Remote Similarity	NPC284865
0.5185	Remote Similarity	NPC603645
0.5172	Remote Similarity	NPC473538
0.5169	Remote Similarity	NPC270667
0.5169	Remote Similarity	NPC164194
0.5139	Remote Similarity	NPC488506
0.5139	Remote Similarity	NPC220498
0.5135	Remote Similarity	NPC229281
0.5132	Remote Similarity	NPC9613
0.5132	Remote Similarity	NPC191412
0.5132	Remote Similarity	NPC114159
0.5132	Remote Similarity	NPC132824
0.5132	Remote Similarity	NPC6818
0.5125	Remote Similarity	NPC54909
0.5109	Remote Similarity	NPC109079
0.5067	Remote Similarity	NPC61543
0.5067	Remote Similarity	NPC38754
0.5067	Remote Similarity	NPC293048
0.5067	Remote Similarity	NPC225585
0.5057	Remote Similarity	NPC43353
0.5056	Remote Similarity	NPC475611
0.5055	Remote Similarity	NPC136877
0.5055	Remote Similarity	NPC12288

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC599947 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6774
0.1-0.2	2327
0.2-0.3	44
0.3-0.4	4
0.4-0.5	1
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