NPASS Compound

Natural Product: NPC612001

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 71 74 0 0 0 0 0 0 0 0999 V2000 6.4849 -1.0183 2.1614 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8271 0.2377 1.5894 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6950 0.1118 0.0888 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0609 1.3539 -0.4600 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6961 1.5742 0.1149 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8403 0.3840 -0.2556 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9039 -0.6730 0.4134 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0089 0.4797 -1.3150 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1446 -0.4879 -1.7979 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8200 -1.7533 -2.1665 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3202 -1.9308 -2.1260 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2222 -2.7511 -2.5345 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5336 0.1002 -3.1293 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6763 0.8713 -2.6987 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7506 0.7001 -1.2206 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1525 0.7181 -0.6798 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6621 2.1733 -0.6405 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0604 2.2316 -0.1328 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2896 1.3413 1.0316 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0479 1.8028 1.9955 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3200 0.9936 3.1673 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6697 1.4703 4.2564 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1565 -0.4699 2.9992 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7801 -0.6763 2.4298 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6803 0.0005 1.0865 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3622 -0.9542 0.1014 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2312 0.1963 0.6924 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4230 -1.0332 0.9617 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0052 -0.8907 0.4380 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1037 -0.6499 -1.0316 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9294 -1.7663 -1.6110 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5233 -0.9444 3.2601 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8686 -1.8937 1.8498 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4706 -1.1447 1.6837 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4393 1.1204 1.8385 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8444 0.3229 2.0762 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7084 0.0097 -0.3836 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1344 -0.8123 -0.1029 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9868 1.3214 -1.5775 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6883 2.2561 -0.2584 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6779 1.6752 1.2032 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2335 2.4716 -0.3854 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6446 -2.4481 -3.0844 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5854 -2.6350 -1.3278 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8667 -0.9927 -2.1114 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3403 0.7577 -3.5336 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2733 -0.6933 -3.8211 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6008 0.6067 -3.2368 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4635 1.9578 -2.8952 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1520 1.4488 -0.7026 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7896 0.2303 -1.4404 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9537 2.8225 -0.1119 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6692 2.4980 -1.7083 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7819 1.9367 -0.9320 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2936 3.2912 0.1079 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4928 2.8171 1.9309 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2835 -1.0063 3.9734 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9690 -0.7932 2.3341 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6502 -1.7796 2.2588 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0243 -0.2973 3.1439 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8482 -1.9358 0.0915 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5392 -0.5130 -0.8813 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3972 -1.2110 0.4826 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8565 0.9887 1.4165 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8923 -1.9514 0.6045 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3238 -1.1277 2.0722 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5255 -1.8089 0.7371 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3960 0.0132 0.9521 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6346 -2.7320 -1.1603 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8474 -1.8518 -2.7048 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0113 -1.6592 -1.3856 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 2 0 6 8 1 0 9 8 1 1 9 10 1 0 10 11 1 0 10 12 2 0 9 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 2 0 21 23 1 0 23 24 1 0 24 25 1 0 25 26 1 6 25 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 6 30 9 1 0 30 15 1 0 27 16 1 0 25 19 1 0 1 32 1 0 1 33 1 0 1 34 1 0 2 35 1 0 2 36 1 0 3 37 1 0 3 38 1 0 4 39 1 0 4 40 1 0 5 41 1 0 5 42 1 0 11 43 1 0 11 44 1 0 11 45 1 0 13 46 1 0 13 47 1 0 14 48 1 0 14 49 1 0 15 50 1 1 16 51 1 6 17 52 1 0 17 53 1 0 18 54 1 0 18 55 1 0 20 56 1 0 23 57 1 0 23 58 1 0 24 59 1 0 24 60 1 0 26 61 1 0 26 62 1 0 26 63 1 0 27 64 1 1 28 65 1 0 28 66 1 0 29 67 1 0 29 68 1 0 31 69 1 0 31 70 1 0 31 71 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 NPC612001 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	21029
0.1-0.2	27029
0.2-0.3	1714
0.3-0.4	50
0.4-0.5	15
0.5-0.6	14
0.6-0.7	1
0.7-0.8	3
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC305039
0.6	Remote Similarity	NPC205860
0.5968	Remote Similarity	NPC317959
0.5484	Remote Similarity	NPC35734
0.5333	Remote Similarity	NPC307176
0.5333	Remote Similarity	NPC321874
0.5323	Remote Similarity	NPC214043
0.5323	Remote Similarity	NPC85774
0.5323	Remote Similarity	NPC282593
0.5312	Remote Similarity	NPC323765
0.5238	Remote Similarity	NPC159577
0.5167	Remote Similarity	NPC139397
0.5079	Remote Similarity	NPC227064
0.5079	Remote Similarity	NPC329043
0.5079	Remote Similarity	NPC58841
0.5079	Remote Similarity	NPC161423

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC612001 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6849
0.1-0.2	2102
0.2-0.3	127
0.3-0.4	32
0.4-0.5	19
0.5-0.6	12
0.6-0.7	4
0.7-0.8	3
0.8-0.85	0
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	NPD6904	Phase 4
0.7333	Intermediate Similarity	NPD6673	Phase 4
0.7049	Intermediate Similarity	NPD6083	Phase 4
0.7049	Intermediate Similarity	NPD6084	Phase 2
0.6087	Remote Similarity	NPD6675	Phase 4
0.6	Remote Similarity	NPD6684	Phase 4
0.6	Remote Similarity	NPD7334	Approved
0.6	Remote Similarity	NPD7521	Phase 4
0.5968	Remote Similarity	NPD6080	Phase 4
0.5797	Remote Similarity	NPD6401	Phase 2
0.5797	Remote Similarity	NPD6402	Phase 4
0.5556	Remote Similarity	NPD7128	Phase 4
0.5333	Remote Similarity	NPD4747	Phase 4
0.5303	Remote Similarity	NPD6409	Approved
0.5231	Remote Similarity	NPD5330	Phase 4
0.5231	Remote Similarity	NPD5694	Approved
0.5217	Remote Similarity	NPD6903	Phase 4
0.5152	Remote Similarity	NPD6050	Phase 4
0.5079	Remote Similarity	NPD3666	Phase 4
0.507	Remote Similarity	NPD7513	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