NPASS Compound

Natural Product: NPC605477

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 61 66 0 0 0 0 0 0 0 0999 V2000 -0.7412 -4.5416 1.6159 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8880 -3.6252 0.5812 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0356 -2.5887 0.2597 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0961 -2.4090 1.0220 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9726 -1.3745 0.7228 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7316 -0.5164 -0.3303 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6939 0.5572 -0.5941 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5155 1.4487 -1.6223 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.4439 -1.8195 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3312 3.2791 -2.7547 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5592 2.5273 -0.9949 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5343 3.4931 -1.1407 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3711 4.4019 -2.1735 O 0 0 0 0 0 0 0 0 0 0 0 0 6.6024 3.5084 -0.2708 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7219 2.5827 0.7423 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8196 2.6182 1.6168 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7430 1.6228 0.8789 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6798 1.6034 0.0174 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7585 0.6878 0.1584 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5947 -0.7183 -1.0751 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2874 -1.7385 -0.7946 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4970 -1.9757 -1.5654 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5310 -2.7998 -2.6697 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3398 -3.4229 -3.0440 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6861 -3.0157 -3.3930 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8359 -2.3761 -2.9812 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0464 -2.5315 -3.6454 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8303 -1.5437 -1.8767 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9531 -0.8904 -1.4367 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0215 -1.0508 -2.0536 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8258 -0.0829 -0.3193 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6463 0.0944 0.3620 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5043 0.9500 1.5488 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2745 1.0768 2.1826 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1091 1.8710 3.2975 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1691 2.5758 3.8300 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0246 3.3835 4.9552 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3870 2.4489 3.2004 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5516 1.6393 2.0653 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5881 -0.5612 -0.1054 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6560 -1.3351 -1.1559 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2402 -5.4454 1.2016 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7651 -4.8758 1.9033 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1573 -4.2090 2.4824 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3744 -3.0246 1.8642 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8711 -1.2317 1.3282 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6538 1.4038 -2.2916 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5264 4.0285 -3.1137 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3618 4.2666 -0.3898 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3373 1.7733 1.8202 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8225 0.8829 1.6746 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3594 -0.0771 -1.9077 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2690 -4.0646 -3.8205 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7211 -3.6590 -4.2581 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6129 -3.3584 -3.4922 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7159 0.4292 0.0217 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4471 0.5249 1.7644 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1447 1.9702 3.7942 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2298 4.3593 4.9395 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2142 2.9997 3.6168 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5491 1.5910 1.6221 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 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 12 14 1 0 14 15 2 0 15 16 1 0 15 17 1 0 17 18 2 0 18 19 1 0 6 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 23 25 1 0 25 26 2 0 26 27 1 0 26 28 1 0 28 29 1 0 29 30 2 0 29 31 1 0 31 32 2 0 32 33 1 0 33 34 2 0 34 35 1 0 35 36 2 0 36 37 1 0 36 38 1 0 38 39 2 0 32 40 1 0 40 41 1 0 21 3 1 0 41 22 1 0 19 7 1 0 41 28 2 0 18 11 1 0 39 33 1 0 1 42 1 0 1 43 1 0 1 44 1 0 4 45 1 0 5 46 1 0 8 47 1 0 13 48 1 0 14 49 1 0 16 50 1 0 17 51 1 0 20 52 1 0 24 53 1 0 25 54 1 0 27 55 1 0 31 56 1 0 34 57 1 0 35 58 1 0 37 59 1 0 38 60 1 0 39 61 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 NPC605477 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	30255
0.1-0.2	16785
0.2-0.3	1812
0.3-0.4	778
0.4-0.5	163
0.5-0.6	32
0.6-0.7	20
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	NPC71061
0.8923	High Similarity	NPC150908
0.8286	Intermediate Similarity	NPC265624
0.8	Intermediate Similarity	NPC215203
0.7714	Intermediate Similarity	NPC72425
0.7714	Intermediate Similarity	NPC303485
0.7361	Intermediate Similarity	NPC14606
0.7313	Intermediate Similarity	NPC138299
0.7123	Intermediate Similarity	NPC186227
0.6986	Remote Similarity	NPC290830
0.6711	Remote Similarity	NPC601565
0.6667	Remote Similarity	NPC194593
0.6615	Remote Similarity	NPC231772
0.6528	Remote Similarity	NPC254351
0.6452	Remote Similarity	NPC50898
0.6447	Remote Similarity	NPC159707
0.64	Remote Similarity	NPC600972
0.6364	Remote Similarity	NPC121649
0.6351	Remote Similarity	NPC259757
0.6349	Remote Similarity	NPC222713
0.6282	Remote Similarity	NPC205026
0.625	Remote Similarity	NPC288840
0.6143	Remote Similarity	NPC67322
0.6087	Remote Similarity	NPC52005
0.6087	Remote Similarity	NPC12200
0.6049	Remote Similarity	NPC55443
0.6026	Remote Similarity	NPC272064
0.6	Remote Similarity	NPC183950
0.6	Remote Similarity	NPC610480
0.589	Remote Similarity	NPC111112
0.5658	Remote Similarity	NPC34089
0.5658	Remote Similarity	NPC183
0.5658	Remote Similarity	NPC196179
0.5652	Remote Similarity	NPC62536
0.5652	Remote Similarity	NPC120464
0.5652	Remote Similarity	NPC483773
0.5652	Remote Similarity	NPC601901
0.5641	Remote Similarity	NPC248739
0.56	Remote Similarity	NPC291746
0.557	Remote Similarity	NPC603508
0.5556	Remote Similarity	NPC610914
0.5522	Remote Similarity	NPC279121
0.5507	Remote Similarity	NPC241498
0.5488	Remote Similarity	NPC18699
0.5455	Remote Similarity	NPC78540
0.5429	Remote Similarity	NPC234133
0.5417	Remote Similarity	NPC606638
0.5405	Remote Similarity	NPC605634
0.5395	Remote Similarity	NPC112954
0.5316	Remote Similarity	NPC606549
0.5309	Remote Similarity	NPC158027
0.5294	Remote Similarity	NPC274121
0.5286	Remote Similarity	NPC301323
0.5286	Remote Similarity	NPC103342
0.5185	Remote Similarity	NPC601984
0.5172	Remote Similarity	NPC604941
0.5139	Remote Similarity	NPC600900
0.507	Remote Similarity	NPC47815
0.506	Remote Similarity	NPC63454
0.506	Remote Similarity	NPC183851
0.5057	Remote Similarity	NPC607079

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC605477 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5989
0.1-0.2	3105
0.2-0.3	48
0.3-0.4	5
0.4-0.5	2
0.5-0.6	1
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
0.5522	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