NPASS Compound

Natural Product: NPC601748

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 32 34 0 0 0 0 0 0 0 0999 V2000 1.8401 -1.4277 -2.6581 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3962 -1.0799 -1.5390 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0098 -1.3113 -1.1173 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5014 0.0103 -0.5435 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9480 0.0152 -0.3079 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5194 -0.6434 0.7530 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8998 -0.6210 0.9520 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7411 0.0586 0.0974 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1216 0.0658 0.3185 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1682 0.7190 -0.9664 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7877 0.6956 -1.1639 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2546 0.2392 0.6315 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6430 0.2239 0.4794 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4652 0.8660 1.4088 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8357 0.8528 1.2617 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6579 1.4886 2.1813 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4497 0.2138 0.2046 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6532 -0.4250 -0.7221 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2037 -1.0883 -1.8113 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2750 -0.4096 -0.5708 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0076 -2.0542 -0.2695 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6558 -1.6818 -1.9114 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1887 0.7889 -1.2784 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8739 -1.1842 1.4371 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3588 -1.1380 1.7865 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6708 0.9322 0.2415 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8200 1.2600 -1.6497 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3816 1.2374 -2.0259 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9795 1.3629 2.2316 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1361 2.3598 1.9664 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5394 0.2139 0.1041 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3250 -0.5395 -2.6553 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 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 2 1 0 11 5 1 0 20 13 1 0 3 21 1 0 3 22 1 0 4 23 1 6 6 24 1 0 7 25 1 0 9 26 1 0 10 27 1 0 11 28 1 0 14 29 1 0 16 30 1 0 17 31 1 0 19 32 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 NPC601748 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	26075
0.1-0.2	19404
0.2-0.3	3284
0.3-0.4	679
0.4-0.5	256
0.5-0.6	104
0.6-0.7	21
0.7-0.8	1
0.8-0.85	6
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC32441
1.0	High Similarity	NPC79943
0.8222	Intermediate Similarity	NPC243083
0.8222	Intermediate Similarity	NPC13768
0.8222	Intermediate Similarity	NPC287246
0.8085	Intermediate Similarity	NPC321011
0.8085	Intermediate Similarity	NPC294852
0.8085	Intermediate Similarity	NPC188679
0.7872	Intermediate Similarity	NPC274784
0.7872	Intermediate Similarity	NPC20709
0.7826	Intermediate Similarity	NPC295261
0.7826	Intermediate Similarity	NPC296490
0.7609	Intermediate Similarity	NPC182421
0.7451	Intermediate Similarity	NPC236637
0.7358	Intermediate Similarity	NPC477841
0.7193	Intermediate Similarity	NPC611447
0.7143	Intermediate Similarity	NPC338131
0.7143	Intermediate Similarity	NPC107586
0.7143	Intermediate Similarity	NPC329203
0.7143	Intermediate Similarity	NPC324386
0.7143	Intermediate Similarity	NPC222342
0.7083	Intermediate Similarity	NPC12296
0.7059	Intermediate Similarity	NPC302950
0.6909	Remote Similarity	NPC109223
0.6909	Remote Similarity	NPC10937
0.6809	Remote Similarity	NPC329225
0.6809	Remote Similarity	NPC147686
0.68	Remote Similarity	NPC300668
0.6735	Remote Similarity	NPC603284
0.6667	Remote Similarity	NPC469764
0.6667	Remote Similarity	NPC606248
0.661	Remote Similarity	NPC69531
0.6531	Remote Similarity	NPC225153
0.6531	Remote Similarity	NPC479876
0.6491	Remote Similarity	NPC134171
0.64	Remote Similarity	NPC201227
0.64	Remote Similarity	NPC258474
0.6364	Remote Similarity	NPC258630
0.6316	Remote Similarity	NPC470135
0.6167	Remote Similarity	NPC312973
0.6102	Remote Similarity	NPC108456
0.6038	Remote Similarity	NPC475267
0.6034	Remote Similarity	NPC17170
0.6	Remote Similarity	NPC482472
0.5968	Remote Similarity	NPC51760
0.5962	Remote Similarity	NPC62290
0.5962	Remote Similarity	NPC142731
0.5962	Remote Similarity	NPC326506
0.5938	Remote Similarity	NPC224851
0.5932	Remote Similarity	NPC106976
0.5926	Remote Similarity	NPC310135
0.5902	Remote Similarity	NPC475790
0.5882	Remote Similarity	NPC476480
0.5882	Remote Similarity	NPC84585
0.5833	Remote Similarity	NPC174953
0.5806	Remote Similarity	NPC88964
0.5789	Remote Similarity	NPC480991
0.5769	Remote Similarity	NPC472460
0.5769	Remote Similarity	NPC264083
0.5769	Remote Similarity	NPC6407
0.5769	Remote Similarity	NPC545184
0.5738	Remote Similarity	NPC134783
0.5714	Remote Similarity	NPC118256
0.5692	Remote Similarity	NPC26195
0.569	Remote Similarity	NPC107572
0.569	Remote Similarity	NPC32739
0.566	Remote Similarity	NPC1612
0.566	Remote Similarity	NPC150648
0.566	Remote Similarity	NPC312391
0.566	Remote Similarity	NPC183959
0.566	Remote Similarity	NPC167624
0.566	Remote Similarity	NPC166482
0.5645	Remote Similarity	NPC470890
0.5645	Remote Similarity	NPC200761
0.5625	Remote Similarity	NPC473272
0.5614	Remote Similarity	NPC484335
0.5556	Remote Similarity	NPC482119
0.5556	Remote Similarity	NPC73028
0.5556	Remote Similarity	NPC473990
0.5556	Remote Similarity	NPC482120
0.5507	Remote Similarity	NPC479054
0.5507	Remote Similarity	NPC602605
0.55	Remote Similarity	NPC470131
0.55	Remote Similarity	NPC470133
0.55	Remote Similarity	NPC220998
0.55	Remote Similarity	NPC470132
0.5472	Remote Similarity	NPC204515
0.5455	Remote Similarity	NPC485881
0.5455	Remote Similarity	NPC210084
0.5455	Remote Similarity	NPC474038
0.5429	Remote Similarity	NPC475184
0.5424	Remote Similarity	NPC39329
0.5424	Remote Similarity	NPC51032
0.5424	Remote Similarity	NPC39045
0.5385	Remote Similarity	NPC265871
0.5385	Remote Similarity	NPC205093
0.5385	Remote Similarity	NPC228504
0.5385	Remote Similarity	NPC474021
0.5373	Remote Similarity	NPC227579
0.5373	Remote Similarity	NPC214166
0.5373	Remote Similarity	NPC475784
0.5352	Remote Similarity	NPC158188
0.5333	Remote Similarity	NPC69674
0.5333	Remote Similarity	NPC271741
0.5323	Remote Similarity	NPC85121
0.5306	Remote Similarity	NPC482958
0.5303	Remote Similarity	NPC472629
0.5303	Remote Similarity	NPC603902
0.5294	Remote Similarity	NPC111786
0.5283	Remote Similarity	NPC188243
0.5283	Remote Similarity	NPC213322
0.5283	Remote Similarity	NPC110228
0.5273	Remote Similarity	NPC255106
0.5273	Remote Similarity	NPC235165
0.5246	Remote Similarity	NPC477840
0.5231	Remote Similarity	NPC272502
0.5224	Remote Similarity	NPC488556
0.5224	Remote Similarity	NPC39351
0.5195	Remote Similarity	NPC476365
0.5195	Remote Similarity	NPC66441
0.5185	Remote Similarity	NPC482121
0.5185	Remote Similarity	NPC270964
0.5172	Remote Similarity	NPC474836
0.5161	Remote Similarity	NPC223500
0.5161	Remote Similarity	NPC486094
0.5147	Remote Similarity	NPC472627
0.5147	Remote Similarity	NPC58805
0.5098	Remote Similarity	NPC93398
0.5098	Remote Similarity	NPC258979
0.5098	Remote Similarity	NPC8283
0.5091	Remote Similarity	NPC20354
0.5091	Remote Similarity	NPC37392
0.5091	Remote Similarity	NPC279417
0.5091	Remote Similarity	NPC49130
0.5088	Remote Similarity	NPC18727
0.5088	Remote Similarity	NPC36835
0.5088	Remote Similarity	NPC246162
0.5088	Remote Similarity	NPC9743
0.5088	Remote Similarity	NPC469758
0.5088	Remote Similarity	NPC260491
0.5088	Remote Similarity	NPC61506
0.5088	Remote Similarity	NPC240476
0.5082	Remote Similarity	NPC221432
0.5082	Remote Similarity	NPC257097
0.5075	Remote Similarity	NPC82330
0.5072	Remote Similarity	NPC74924
0.5072	Remote Similarity	NPC67396
0.5063	Remote Similarity	NPC182555

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC601748 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4582
0.1-0.2	4431
0.2-0.3	121
0.3-0.4	4
0.4-0.5	8
0.5-0.6	0
0.6-0.7	1
0.7-0.8	1
0.8-0.85	1
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	NPD1552	Clinical (unspecified phase)
0.8222	Intermediate Similarity	NPD1550	Phase 2
0.7059	Intermediate Similarity	NPD1934	Phase 0
0.6809	Remote Similarity	NPD1549	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