NPASS Compound

Natural Product: NPC611838

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 55 58 0 0 0 0 0 0 0 0999 V2000 5.9202 -0.7994 -0.4854 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5001 -0.6417 -0.9117 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2698 -0.6057 -2.1095 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4771 -0.5406 0.1362 C 0 0 1 0 0 0 0 0 0 0 0 0 3.7110 0.6483 1.0468 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3218 1.1161 1.4985 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3914 0.1714 0.8617 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0037 0.6181 0.6471 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6631 0.9144 1.9448 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0347 0.3628 2.0822 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7435 -0.1415 1.1153 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0995 -0.6683 1.3413 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9371 -0.4731 0.1176 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1640 0.9184 -0.0071 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2994 -1.0773 -1.0824 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8310 -1.3056 -1.0064 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1725 -0.1939 -0.2520 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3233 1.0929 -1.0242 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7125 -0.5507 -0.0517 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0265 -0.9552 -1.3109 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3992 -1.3368 -1.0399 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1072 -0.1789 -0.4349 C 0 0 2 0 0 0 0 0 0 0 0 0 2.2228 0.9714 -1.3744 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4797 -1.5013 -1.1117 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3792 0.2060 -0.5022 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9798 -1.1676 0.5780 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3449 -1.4832 0.7228 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3533 0.3885 1.9092 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1382 1.4595 0.4257 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2936 0.9883 2.5986 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1622 2.1806 1.2648 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3670 -0.7730 1.4592 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0632 1.5348 0.0188 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0621 0.4474 2.7786 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7049 1.9902 2.1524 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4691 0.3896 3.0794 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0175 -1.7663 1.5993 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5676 -0.1772 2.2296 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9230 -0.9689 0.3022 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3052 1.2376 0.9305 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8367 -2.0320 -1.3374 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5078 -0.4098 -1.9552 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4312 -1.2534 -2.0584 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5585 -2.3096 -0.6114 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1017 1.0383 -1.8085 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3855 1.3535 -1.5700 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6210 1.8853 -0.3146 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6848 -1.3921 0.6707 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5343 -1.8811 -1.6740 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1346 -0.1959 -2.1052 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3909 -2.2010 -0.3451 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8508 -1.6853 -1.9967 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2710 1.3899 -1.4188 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0353 0.5917 -2.4212 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5527 1.8097 -1.1907 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 1 0 13 14 1 0 13 15 1 0 15 16 1 0 16 17 1 0 17 18 1 6 17 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 6 22 4 1 0 22 7 1 0 19 8 1 0 17 11 1 0 1 24 1 0 1 25 1 0 1 26 1 0 4 27 1 1 5 28 1 0 5 29 1 0 6 30 1 0 6 31 1 0 7 32 1 1 8 33 1 6 9 34 1 0 9 35 1 0 10 36 1 0 12 37 1 0 12 38 1 0 13 39 1 1 14 40 1 0 15 41 1 0 15 42 1 0 16 43 1 0 16 44 1 0 18 45 1 0 18 46 1 0 18 47 1 0 19 48 1 1 20 49 1 0 20 50 1 0 21 51 1 0 21 52 1 0 23 53 1 0 23 54 1 0 23 55 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 NPC611838 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	16870
0.1-0.2	26019
0.2-0.3	6509
0.3-0.4	303
0.4-0.5	77
0.5-0.6	30
0.6-0.7	38
0.7-0.8	0
0.8-0.85	0
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	NPC221758
0.8571	High Similarity	NPC51014
0.7451	Intermediate Similarity	NPC328313
0.7222	Intermediate Similarity	NPC472265
0.7222	Intermediate Similarity	NPC33913
0.7222	Intermediate Similarity	NPC59453
0.7059	Intermediate Similarity	NPC162742
0.7059	Intermediate Similarity	NPC304309
0.7059	Intermediate Similarity	NPC470228
0.6923	Remote Similarity	NPC22105
0.6923	Remote Similarity	NPC34019
0.6923	Remote Similarity	NPC107059
0.6923	Remote Similarity	NPC600590
0.6792	Remote Similarity	NPC136188
0.6792	Remote Similarity	NPC28657
0.6792	Remote Similarity	NPC474216
0.6792	Remote Similarity	NPC154330
0.6667	Remote Similarity	NPC243985
0.6667	Remote Similarity	NPC230301
0.6667	Remote Similarity	NPC280710
0.6667	Remote Similarity	NPC240650
0.6667	Remote Similarity	NPC113733
0.6667	Remote Similarity	NPC198968
0.6667	Remote Similarity	NPC285893
0.6667	Remote Similarity	NPC134847
0.6604	Remote Similarity	NPC151519
0.6545	Remote Similarity	NPC241290
0.6545	Remote Similarity	NPC164840
0.6545	Remote Similarity	NPC484739
0.6545	Remote Similarity	NPC209944
0.6545	Remote Similarity	NPC264245
0.6545	Remote Similarity	NPC155986
0.65	Remote Similarity	NPC601043
0.65	Remote Similarity	NPC605412
0.6491	Remote Similarity	NPC603646
0.6481	Remote Similarity	NPC20688
0.6429	Remote Similarity	NPC328714
0.6429	Remote Similarity	NPC321381
0.6379	Remote Similarity	NPC473943
0.6379	Remote Similarity	NPC155011
0.6364	Remote Similarity	NPC76879
0.6316	Remote Similarity	NPC318495
0.6275	Remote Similarity	NPC96319
0.6271	Remote Similarity	NPC47761
0.6271	Remote Similarity	NPC488870
0.6	Remote Similarity	NPC21667
0.6	Remote Similarity	NPC474164
0.5763	Remote Similarity	NPC1272
0.5763	Remote Similarity	NPC470614
0.5667	Remote Similarity	NPC477522
0.5606	Remote Similarity	NPC309493
0.5385	Remote Similarity	NPC5985
0.5373	Remote Similarity	NPC235126
0.5373	Remote Similarity	NPC242419
0.5333	Remote Similarity	NPC26959
0.5312	Remote Similarity	NPC474970
0.5312	Remote Similarity	NPC474349
0.5312	Remote Similarity	NPC474189
0.5294	Remote Similarity	NPC147835
0.5294	Remote Similarity	NPC253645
0.5294	Remote Similarity	NPC85001
0.5294	Remote Similarity	NPC95920
0.5231	Remote Similarity	NPC176012
0.5217	Remote Similarity	NPC486119
0.5185	Remote Similarity	NPC320549
0.5185	Remote Similarity	NPC156277
0.5185	Remote Similarity	NPC58057
0.5185	Remote Similarity	NPC151018
0.5161	Remote Similarity	NPC58063
0.5085	Remote Similarity	NPC98765
0.5082	Remote Similarity	NPC31564
0.5082	Remote Similarity	NPC87604
0.5082	Remote Similarity	NPC145879
0.5079	Remote Similarity	NPC268406
0.5075	Remote Similarity	NPC91604
0.507	Remote Similarity	NPC3715
0.507	Remote Similarity	NPC212874

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC611838 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6120
0.1-0.2	2733
0.2-0.3	251
0.3-0.4	32
0.4-0.5	5
0.5-0.6	3
0.6-0.7	4
0.7-0.8	0
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	NPD4786	Phase 1
0.6792	Remote Similarity	NPD6942	Phase 4
0.6667	Remote Similarity	NPD7339	Approved
0.6604	Remote Similarity	NPD3667	Phase 4
0.6275	Remote Similarity	NPD3701	Pre-clinical
0.5469	Remote Similarity	NPD6399	Phase 3
0.5185	Remote Similarity	NPD4808	Phase 2
0.5185	Remote Similarity	NPD4809	Phase 4

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