NPASS Compound

Natural Product: NPC602287

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 34 36 0 0 0 0 0 0 0 0999 V2000 1.1741 -3.2705 0.1856 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7145 -2.2282 1.0482 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1029 -1.2261 0.6425 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3692 -0.0288 0.1940 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7668 0.3540 0.0930 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8046 -0.3412 0.6435 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1387 0.0625 0.4697 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4583 1.1644 -0.2534 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7935 1.5530 -0.4169 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4374 1.8820 -0.8162 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1372 1.4836 -0.6442 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4996 0.9214 -0.2050 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7848 0.7515 -0.1810 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6139 1.7796 -0.6088 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9874 1.6595 -0.6069 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8176 2.7022 -1.0403 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5220 0.4672 -0.1597 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7217 -0.5710 0.2711 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2917 -1.7564 0.7145 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3496 -0.4218 0.2577 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4852 -1.4117 0.6707 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9647 -2.5047 1.0810 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3476 -3.9285 -0.1289 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7261 -2.8151 -0.6385 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8680 -3.8854 0.8004 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6647 -1.2040 1.2520 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9270 -0.5083 0.9156 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0745 2.4606 -0.0201 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7001 2.7592 -1.3908 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3510 2.0632 -1.0968 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1761 2.6992 -0.9529 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9996 3.5121 -0.4642 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6079 0.3499 -0.1493 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5290 -2.5233 0.1120 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 8 10 1 0 10 11 2 0 4 12 1 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 15 17 2 0 17 18 1 0 18 19 1 0 18 20 2 0 20 21 1 0 21 22 2 0 21 3 1 0 11 5 1 0 20 13 1 0 1 23 1 0 1 24 1 0 1 25 1 0 6 26 1 0 7 27 1 0 9 28 1 0 10 29 1 0 11 30 1 0 14 31 1 0 16 32 1 0 17 33 1 0 19 34 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 NPC602287 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	29637
0.1-0.2	16615
0.2-0.3	2293
0.3-0.4	755
0.4-0.5	348
0.5-0.6	134
0.6-0.7	31
0.7-0.8	0
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC103342
0.8571	High Similarity	NPC286342
0.8367	Intermediate Similarity	NPC184536
0.82	Intermediate Similarity	NPC59951
0.7925	Intermediate Similarity	NPC279989
0.7647	Intermediate Similarity	NPC123886
0.7547	Intermediate Similarity	NPC82325
0.75	Intermediate Similarity	NPC610359
0.7407	Intermediate Similarity	NPC603596
0.7308	Intermediate Similarity	NPC266960
0.717	Intermediate Similarity	NPC146679
0.7091	Intermediate Similarity	NPC162351
0.6792	Remote Similarity	NPC136840
0.6774	Remote Similarity	NPC269285
0.6667	Remote Similarity	NPC54802
0.6667	Remote Similarity	NPC197304
0.661	Remote Similarity	NPC158874
0.6562	Remote Similarity	NPC288084
0.6545	Remote Similarity	NPC101830
0.6364	Remote Similarity	NPC111929
0.6364	Remote Similarity	NPC320283
0.6364	Remote Similarity	NPC41121
0.6269	Remote Similarity	NPC104677
0.6269	Remote Similarity	NPC77672
0.6269	Remote Similarity	NPC470461
0.6269	Remote Similarity	NPC133671
0.6269	Remote Similarity	NPC135391
0.6269	Remote Similarity	NPC78263
0.6269	Remote Similarity	NPC250069
0.625	Remote Similarity	NPC214138
0.625	Remote Similarity	NPC105242
0.625	Remote Similarity	NPC163524
0.625	Remote Similarity	NPC605144
0.619	Remote Similarity	NPC97255
0.6129	Remote Similarity	NPC306488
0.6094	Remote Similarity	NPC56786
0.6071	Remote Similarity	NPC191459
0.6071	Remote Similarity	NPC287979
0.6071	Remote Similarity	NPC90582
0.6038	Remote Similarity	NPC50898
0.6038	Remote Similarity	NPC116775
0.6	Remote Similarity	NPC216496
0.6	Remote Similarity	NPC470458
0.5965	Remote Similarity	NPC149127
0.5965	Remote Similarity	NPC260895
0.5965	Remote Similarity	NPC176665
0.5965	Remote Similarity	NPC188871
0.5965	Remote Similarity	NPC606763
0.5915	Remote Similarity	NPC159579
0.5915	Remote Similarity	NPC129217
0.5915	Remote Similarity	NPC48093
0.5833	Remote Similarity	NPC183950
0.5833	Remote Similarity	NPC125062
0.5833	Remote Similarity	NPC85707
0.5833	Remote Similarity	NPC259957
0.5833	Remote Similarity	NPC224530
0.5821	Remote Similarity	NPC276222
0.5821	Remote Similarity	NPC274618
0.5821	Remote Similarity	NPC118284
0.5821	Remote Similarity	NPC608147
0.5818	Remote Similarity	NPC179271
0.5789	Remote Similarity	NPC203891
0.5789	Remote Similarity	NPC103904
0.5789	Remote Similarity	NPC262094
0.5763	Remote Similarity	NPC54394
0.5763	Remote Similarity	NPC178343
0.5735	Remote Similarity	NPC67037
0.5735	Remote Similarity	NPC255615
0.5714	Remote Similarity	NPC153512
0.5692	Remote Similarity	NPC259632
0.569	Remote Similarity	NPC50403
0.569	Remote Similarity	NPC231772
0.569	Remote Similarity	NPC241838
0.569	Remote Similarity	NPC601901
0.5676	Remote Similarity	NPC170052
0.5676	Remote Similarity	NPC476215
0.5676	Remote Similarity	NPC135846
0.5667	Remote Similarity	NPC52005
0.5636	Remote Similarity	NPC20791
0.5634	Remote Similarity	NPC52550
0.5614	Remote Similarity	NPC230285
0.5614	Remote Similarity	NPC245546
0.5593	Remote Similarity	NPC9609
0.5593	Remote Similarity	NPC305663
0.5593	Remote Similarity	NPC18772
0.5574	Remote Similarity	NPC78326
0.5571	Remote Similarity	NPC127546
0.5571	Remote Similarity	NPC57625
0.5571	Remote Similarity	NPC173637
0.5571	Remote Similarity	NPC317489
0.5571	Remote Similarity	NPC223424
0.5571	Remote Similarity	NPC600591
0.5556	Remote Similarity	NPC472459
0.5541	Remote Similarity	NPC223747
0.5536	Remote Similarity	NPC279121
0.5517	Remote Similarity	NPC219330
0.55	Remote Similarity	NPC253634
0.55	Remote Similarity	NPC159103
0.5493	Remote Similarity	NPC145038
0.5493	Remote Similarity	NPC56077
0.5493	Remote Similarity	NPC281131
0.5493	Remote Similarity	NPC470460
0.5493	Remote Similarity	NPC253662
0.5493	Remote Similarity	NPC179950
0.5493	Remote Similarity	NPC88789
0.5493	Remote Similarity	NPC491374
0.5479	Remote Similarity	NPC175107
0.5467	Remote Similarity	NPC203050
0.5467	Remote Similarity	NPC225434
0.5455	Remote Similarity	NPC471079
0.5455	Remote Similarity	NPC139320
0.5424	Remote Similarity	NPC62536
0.5424	Remote Similarity	NPC28274
0.5424	Remote Similarity	NPC120464
0.5424	Remote Similarity	NPC483773
0.541	Remote Similarity	NPC236223
0.541	Remote Similarity	NPC12200
0.541	Remote Similarity	NPC606638
0.541	Remote Similarity	NPC609179
0.5405	Remote Similarity	NPC609478
0.5385	Remote Similarity	NPC173582
0.5385	Remote Similarity	NPC470405
0.5385	Remote Similarity	NPC265885
0.5385	Remote Similarity	NPC181465
0.5385	Remote Similarity	NPC215710
0.5385	Remote Similarity	NPC163242
0.5385	Remote Similarity	NPC272068
0.5385	Remote Similarity	NPC473438
0.5385	Remote Similarity	NPC253788
0.5362	Remote Similarity	NPC600972
0.5345	Remote Similarity	NPC472438
0.5342	Remote Similarity	NPC80534
0.5333	Remote Similarity	NPC22472
0.5333	Remote Similarity	NPC607913
0.5323	Remote Similarity	NPC133953
0.5316	Remote Similarity	NPC304741
0.5286	Remote Similarity	NPC290830
0.5286	Remote Similarity	NPC71061
0.5286	Remote Similarity	NPC72425
0.5278	Remote Similarity	NPC64305
0.5278	Remote Similarity	NPC265530
0.527	Remote Similarity	NPC235260
0.527	Remote Similarity	NPC155763
0.527	Remote Similarity	NPC219904
0.5254	Remote Similarity	NPC301323
0.5254	Remote Similarity	NPC43243
0.5254	Remote Similarity	NPC241498
0.525	Remote Similarity	NPC129264
0.5246	Remote Similarity	NPC115798
0.5246	Remote Similarity	NPC470216
0.5246	Remote Similarity	NPC270620
0.5246	Remote Similarity	NPC29841
0.5211	Remote Similarity	NPC272064
0.52	Remote Similarity	NPC120099
0.5185	Remote Similarity	NPC61904
0.5185	Remote Similarity	NPC470125
0.5185	Remote Similarity	NPC296018
0.5167	Remote Similarity	NPC110070
0.5167	Remote Similarity	NPC143799
0.5167	Remote Similarity	NPC76376
0.5167	Remote Similarity	NPC130894
0.5167	Remote Similarity	NPC610660
0.5161	Remote Similarity	NPC18607
0.5161	Remote Similarity	NPC236769
0.5143	Remote Similarity	NPC34531
0.5139	Remote Similarity	NPC215203
0.5135	Remote Similarity	NPC325555
0.5135	Remote Similarity	NPC226304
0.5122	Remote Similarity	NPC297503
0.5122	Remote Similarity	NPC12013
0.5122	Remote Similarity	NPC11432
0.5122	Remote Similarity	NPC477613
0.5082	Remote Similarity	NPC600900
0.5079	Remote Similarity	NPC261004
0.506	Remote Similarity	NPC270448
0.506	Remote Similarity	NPC104883
0.506	Remote Similarity	NPC488679

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC602287 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5655
0.1-0.2	3416
0.2-0.3	68
0.3-0.4	7
0.4-0.5	2
0.5-0.6	2
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
0.5636	Remote Similarity	NPD1512	Phase 3
0.5536	Remote Similarity	NPD1511	Phase 2

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