NPASS Compound

Natural Product: NPC612073

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 31 33 0 0 0 0 0 0 0 0999 V2000 2.2824 -2.5070 -1.2693 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4164 -1.6476 -0.9582 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0207 -1.7911 -1.1999 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7130 -0.4959 -1.5340 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8967 -0.2602 -0.6762 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1554 -0.5265 -1.1561 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2874 -0.3123 -0.3660 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0817 0.1785 0.9169 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8424 0.4529 1.4226 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7456 0.2223 0.5947 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1094 0.6458 -1.3839 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2090 0.7359 -0.5567 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6229 1.9190 0.0215 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7368 1.8888 0.8303 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1509 3.0821 1.4112 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4492 0.7373 1.0843 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0266 -0.4366 0.5020 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6801 -1.6489 0.6978 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9124 -0.4395 -0.3143 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2658 -2.5663 -1.9553 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4612 -2.1227 -0.2098 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0331 -0.5933 -2.6130 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3181 -0.9091 -2.1559 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2837 -0.5148 -0.7237 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9484 0.3516 1.5465 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7433 0.8289 2.4164 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7584 0.4376 0.9886 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0547 2.8131 -0.1867 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8790 3.3138 2.3595 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3177 0.7446 1.7219 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7076 -1.5803 0.7449 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 9 10 2 0 4 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 1 0 14 16 2 0 16 17 1 0 17 18 1 0 17 19 2 0 19 2 1 0 10 5 1 0 19 12 1 0 3 20 1 0 3 21 1 0 4 22 1 6 6 23 1 0 7 24 1 0 8 25 1 0 9 26 1 0 10 27 1 0 13 28 1 0 15 29 1 0 16 30 1 0 18 31 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 NPC612073 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	24789
0.1-0.2	21352
0.2-0.3	2864
0.3-0.4	560
0.4-0.5	170
0.5-0.6	73
0.6-0.7	25
0.7-0.8	1
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC243083
1.0	High Similarity	NPC13768
1.0	High Similarity	NPC287246
0.8222	Intermediate Similarity	NPC32441
0.8222	Intermediate Similarity	NPC79943
0.7872	Intermediate Similarity	NPC274784
0.7872	Intermediate Similarity	NPC20709
0.7609	Intermediate Similarity	NPC182421
0.75	Intermediate Similarity	NPC107586
0.7347	Intermediate Similarity	NPC321011
0.7347	Intermediate Similarity	NPC294852
0.7347	Intermediate Similarity	NPC188679
0.7143	Intermediate Similarity	NPC338131
0.7083	Intermediate Similarity	NPC295261
0.7083	Intermediate Similarity	NPC296490
0.7083	Intermediate Similarity	NPC12296
0.7059	Intermediate Similarity	NPC302950
0.6939	Remote Similarity	NPC150648
0.6939	Remote Similarity	NPC312391
0.68	Remote Similarity	NPC482119
0.68	Remote Similarity	NPC482120
0.6792	Remote Similarity	NPC236637
0.6735	Remote Similarity	NPC204515
0.6727	Remote Similarity	NPC477841
0.6667	Remote Similarity	NPC265871
0.6667	Remote Similarity	NPC205093
0.6531	Remote Similarity	NPC476480
0.6531	Remote Similarity	NPC213322
0.6531	Remote Similarity	NPC84585
0.6471	Remote Similarity	NPC255106
0.6471	Remote Similarity	NPC235165
0.64	Remote Similarity	NPC482121
0.64	Remote Similarity	NPC270964
0.6364	Remote Similarity	NPC258630
0.6316	Remote Similarity	NPC109223
0.6316	Remote Similarity	NPC10937
0.6275	Remote Similarity	NPC37392
0.625	Remote Similarity	NPC39045
0.6154	Remote Similarity	NPC194432
0.6102	Remote Similarity	NPC108456
0.6066	Remote Similarity	NPC611447
0.6034	Remote Similarity	NPC17170
0.5965	Remote Similarity	NPC1089
0.5962	Remote Similarity	NPC4152
0.5932	Remote Similarity	NPC106976
0.5902	Remote Similarity	NPC312973
0.5902	Remote Similarity	NPC475790
0.5849	Remote Similarity	NPC329203
0.5849	Remote Similarity	NPC324386
0.5849	Remote Similarity	NPC222342
0.5833	Remote Similarity	NPC174953
0.5769	Remote Similarity	NPC6407
0.5769	Remote Similarity	NPC545184
0.5763	Remote Similarity	NPC470135
0.5738	Remote Similarity	NPC134783
0.5714	Remote Similarity	NPC35150
0.5714	Remote Similarity	NPC106328
0.5692	Remote Similarity	NPC26195
0.566	Remote Similarity	NPC177354
0.5645	Remote Similarity	NPC470890
0.5645	Remote Similarity	NPC200761
0.5577	Remote Similarity	NPC225153
0.5577	Remote Similarity	NPC188243
0.5577	Remote Similarity	NPC479876
0.5577	Remote Similarity	NPC110228
0.5556	Remote Similarity	NPC99597
0.5556	Remote Similarity	NPC300668
0.5556	Remote Similarity	NPC73028
0.5556	Remote Similarity	NPC473990
0.5556	Remote Similarity	NPC69531
0.5536	Remote Similarity	NPC609747
0.5517	Remote Similarity	NPC76372
0.5517	Remote Similarity	NPC37496
0.549	Remote Similarity	NPC329225
0.549	Remote Similarity	NPC147686
0.5472	Remote Similarity	NPC248372
0.5472	Remote Similarity	NPC482487
0.5472	Remote Similarity	NPC603284
0.5469	Remote Similarity	NPC118256
0.5455	Remote Similarity	NPC469764
0.5455	Remote Similarity	NPC606248
0.5424	Remote Similarity	NPC109183
0.5417	Remote Similarity	NPC314329
0.5417	Remote Similarity	NPC603208
0.541	Remote Similarity	NPC134171
0.5385	Remote Similarity	NPC473272
0.5385	Remote Similarity	NPC474021
0.5357	Remote Similarity	NPC310135
0.5333	Remote Similarity	NPC295650
0.5333	Remote Similarity	NPC175504
0.5323	Remote Similarity	NPC85121
0.5312	Remote Similarity	NPC88964
0.5306	Remote Similarity	NPC228184
0.5273	Remote Similarity	NPC215885
0.5273	Remote Similarity	NPC110776
0.5273	Remote Similarity	NPC110038
0.5246	Remote Similarity	NPC176229
0.5224	Remote Similarity	NPC474038
0.5185	Remote Similarity	NPC472460
0.5185	Remote Similarity	NPC201227
0.5185	Remote Similarity	NPC258474
0.5185	Remote Similarity	NPC264083
0.5147	Remote Similarity	NPC227579
0.5147	Remote Similarity	NPC214166
0.5147	Remote Similarity	NPC475784
0.5091	Remote Similarity	NPC20354
0.5088	Remote Similarity	NPC18727
0.5088	Remote Similarity	NPC2416
0.5088	Remote Similarity	NPC469758
0.5088	Remote Similarity	NPC271590
0.5082	Remote Similarity	NPC122894
0.5075	Remote Similarity	NPC97052
0.5072	Remote Similarity	NPC74924
0.5072	Remote Similarity	NPC111786
0.507	Remote Similarity	NPC602605

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC612073 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3796
0.1-0.2	5123
0.2-0.3	211
0.3-0.4	15
0.4-0.5	0
0.5-0.6	2
0.6-0.7	0
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	NPD1550	Phase 2
0.8222	Intermediate Similarity	NPD1552	Clinical (unspecified phase)
0.7059	Intermediate Similarity	NPD1934	Phase 0
0.549	Remote Similarity	NPD1549	Phase 2
0.5417	Remote Similarity	NPD1547	Clinical (unspecified phase)

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