NPASS Compound

Natural Product: NPC611009

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 52 51 0 0 0 0 0 0 0 0999 V2000 8.8897 -0.4984 -0.9205 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5400 -0.3869 -0.2460 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0842 1.0572 -0.2852 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7549 1.2505 0.3677 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6406 0.4377 -0.2910 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4017 0.7488 0.4889 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7187 -0.2061 1.1168 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4986 0.0727 1.8914 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2878 -0.6458 1.3925 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7890 -0.0235 0.9790 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9946 -0.7804 0.4821 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3084 -0.4137 -0.9296 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4784 -1.0629 -1.5077 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8621 -0.7870 -1.0877 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2158 -0.9864 0.3121 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6431 -0.8307 0.7391 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3202 0.4492 0.5624 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5811 0.8477 -0.8064 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6298 0.0063 -1.7351 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7944 2.1856 -1.1832 O 0 0 0 0 0 0 0 0 0 0 0 0 9.0392 0.3517 -1.6127 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0008 -1.4641 -1.4730 H 0 0 0 0 0 0 0 0 0 0 0 0 9.7033 -0.4534 -0.1468 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6770 -0.6618 0.8190 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7878 -1.0613 -0.7090 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8166 1.6697 0.2678 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0415 1.4505 -1.3108 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4794 2.3236 0.2632 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7666 0.9288 1.4303 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5233 0.7432 -1.3322 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8563 -0.6356 -0.1462 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0055 1.7632 0.5776 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1249 -1.2122 1.0181 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3004 1.1465 2.0227 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6811 -0.3348 2.9301 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3202 -1.7174 1.3793 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7836 1.0656 1.0062 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7656 -0.8448 1.2136 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5957 -1.8629 0.4000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2998 0.7084 -1.0737 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3683 -0.7115 -1.5176 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4636 -0.8352 -2.6422 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2896 -2.2061 -1.5654 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0719 0.2691 -1.4519 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5056 -1.5130 -1.6976 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6950 -0.1893 0.9732 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8323 -1.9474 0.6906 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7161 -1.1312 1.8320 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2723 -1.6299 0.2311 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3461 0.3574 1.0630 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8608 1.2873 1.1710 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4568 2.3472 -1.9493 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 7 8 1 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 1 0 12 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 2 0 18 20 1 0 1 21 1 0 1 22 1 0 1 23 1 0 2 24 1 0 2 25 1 0 3 26 1 0 3 27 1 0 4 28 1 0 4 29 1 0 5 30 1 0 5 31 1 0 6 32 1 0 7 33 1 0 8 34 1 0 8 35 1 0 9 36 1 0 10 37 1 0 11 38 1 0 11 39 1 0 12 40 1 0 12 41 1 0 13 42 1 0 13 43 1 0 14 44 1 0 14 45 1 0 15 46 1 0 15 47 1 0 16 48 1 0 16 49 1 0 17 50 1 0 17 51 1 0 20 52 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 NPC611009 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	38005
0.1-0.2	10145
0.2-0.3	1275
0.3-0.4	224
0.4-0.5	82
0.5-0.6	46
0.6-0.7	50
0.7-0.8	2
0.8-0.85	6
0.85-0.9	15
0.9-0.95	1
0.95-1	5

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC154245
1.0	High Similarity	NPC85813
1.0	High Similarity	NPC223697
1.0	High Similarity	NPC6095
0.9655	High Similarity	NPC321062
0.9	High Similarity	NPC5413
0.8966	High Similarity	NPC424
0.8966	High Similarity	NPC36061
0.8966	High Similarity	NPC69510
0.8966	High Similarity	NPC77272
0.8966	High Similarity	NPC290563
0.8966	High Similarity	NPC139029
0.8966	High Similarity	NPC281972
0.8966	High Similarity	NPC261831
0.8966	High Similarity	NPC87564
0.871	High Similarity	NPC52955
0.871	High Similarity	NPC88966
0.871	High Similarity	NPC25417
0.871	High Similarity	NPC1813
0.871	High Similarity	NPC59051
0.8621	High Similarity	NPC281245
0.8387	Intermediate Similarity	NPC91495
0.8387	Intermediate Similarity	NPC70387
0.8333	Intermediate Similarity	NPC92114
0.8065	Intermediate Similarity	NPC95145
0.8065	Intermediate Similarity	NPC325642
0.8065	Intermediate Similarity	NPC65174
0.75	Intermediate Similarity	NPC149821
0.697	Remote Similarity	NPC207292
0.6897	Remote Similarity	NPC171736
0.6897	Remote Similarity	NPC301585
0.6897	Remote Similarity	NPC261080
0.6897	Remote Similarity	NPC132565
0.6897	Remote Similarity	NPC209970
0.6897	Remote Similarity	NPC216630
0.6897	Remote Similarity	NPC201844
0.6897	Remote Similarity	NPC301696
0.6897	Remote Similarity	NPC196924
0.6897	Remote Similarity	NPC307783
0.6897	Remote Similarity	NPC154186
0.6897	Remote Similarity	NPC149184
0.6897	Remote Similarity	NPC279026
0.6897	Remote Similarity	NPC113928
0.6897	Remote Similarity	NPC14227
0.6842	Remote Similarity	NPC477201
0.6585	Remote Similarity	NPC320642
0.6585	Remote Similarity	NPC329550
0.6552	Remote Similarity	NPC155263
0.65	Remote Similarity	NPC323597
0.65	Remote Similarity	NPC211752
0.65	Remote Similarity	NPC243532
0.65	Remote Similarity	NPC323498
0.6429	Remote Similarity	NPC323045
0.6429	Remote Similarity	NPC317881
0.641	Remote Similarity	NPC106851
0.641	Remote Similarity	NPC282788
0.641	Remote Similarity	NPC274927
0.6364	Remote Similarity	NPC117572
0.6341	Remote Similarity	NPC317583
0.6341	Remote Similarity	NPC68343
0.6341	Remote Similarity	NPC328089
0.6316	Remote Similarity	NPC606120
0.6286	Remote Similarity	NPC224227
0.6279	Remote Similarity	NPC322461
0.625	Remote Similarity	NPC180534
0.625	Remote Similarity	NPC179764
0.625	Remote Similarity	NPC611531
0.6136	Remote Similarity	NPC605544
0.6136	Remote Similarity	NPC607260
0.6098	Remote Similarity	NPC251042
0.6098	Remote Similarity	NPC255863
0.6098	Remote Similarity	NPC473863
0.6098	Remote Similarity	NPC174447
0.6098	Remote Similarity	NPC136164
0.6098	Remote Similarity	NPC122521
0.6098	Remote Similarity	NPC245947
0.6	Remote Similarity	NPC329249
0.6	Remote Similarity	NPC92558
0.5952	Remote Similarity	NPC318420
0.5952	Remote Similarity	NPC326268
0.5897	Remote Similarity	NPC487561
0.5897	Remote Similarity	NPC225929
0.5882	Remote Similarity	NPC34416
0.5862	Remote Similarity	NPC214610
0.5862	Remote Similarity	NPC118968
0.5862	Remote Similarity	NPC183424
0.5862	Remote Similarity	NPC294085
0.5833	Remote Similarity	NPC87394
0.5814	Remote Similarity	NPC325977
0.5814	Remote Similarity	NPC327112
0.5714	Remote Similarity	NPC8219
0.5682	Remote Similarity	NPC328311
0.5667	Remote Similarity	NPC175342
0.5581	Remote Similarity	NPC320305
0.5581	Remote Similarity	NPC321838
0.5556	Remote Similarity	NPC18712
0.5556	Remote Similarity	NPC74845
0.5517	Remote Similarity	NPC268826
0.5429	Remote Similarity	NPC262968
0.5405	Remote Similarity	NPC294548
0.5405	Remote Similarity	NPC48162
0.5405	Remote Similarity	NPC324004
0.5405	Remote Similarity	NPC328497
0.5405	Remote Similarity	NPC602547
0.5385	Remote Similarity	NPC40082
0.5349	Remote Similarity	NPC187777
0.5349	Remote Similarity	NPC318814
0.5349	Remote Similarity	NPC320669
0.5333	Remote Similarity	NPC49863
0.5294	Remote Similarity	NPC55023
0.5294	Remote Similarity	NPC21844
0.5278	Remote Similarity	NPC129972
0.5278	Remote Similarity	NPC301528
0.5278	Remote Similarity	NPC71317
0.5278	Remote Similarity	NPC163746
0.5278	Remote Similarity	NPC103286
0.5263	Remote Similarity	NPC174560
0.5263	Remote Similarity	NPC125312
0.5172	Remote Similarity	NPC174368
0.5152	Remote Similarity	NPC604140
0.5122	Remote Similarity	NPC323436
0.5122	Remote Similarity	NPC327388
0.5122	Remote Similarity	NPC284212
0.5116	Remote Similarity	NPC274290

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC611009 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6801
0.1-0.2	2111
0.2-0.3	179
0.3-0.4	31
0.4-0.5	8
0.5-0.6	7
0.6-0.7	5
0.7-0.8	2
0.8-0.85	0
0.85-0.9	3
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD4266	Phase 2
0.9	High Similarity	NPD3173	Phase 4
0.8966	High Similarity	NPD3195	Phase 2
0.8966	High Similarity	NPD3196	Approved
0.871	High Similarity	NPD3172	Approved
0.7632	Intermediate Similarity	NPD39	Phase 4
0.7222	Intermediate Similarity	NPD3194	Phase 4
0.6897	Remote Similarity	NPD2270	Pre-clinical
0.6897	Remote Similarity	NPD633	Phase 3
0.6897	Remote Similarity	NPD9448	Phase 2
0.6364	Remote Similarity	NPD4222	Phase 3
0.625	Remote Similarity	NPD622	Pre-clinical
0.5862	Remote Similarity	NPD9655	Phase 4
0.5814	Remote Similarity	NPD4246	Phase 2
0.5556	Remote Similarity	NPD3174	Discontinued
0.5429	Remote Similarity	NPD28	Approved
0.5429	Remote Similarity	NPD29	Phase 4
0.5405	Remote Similarity	NPD3199	Clinical (unspecified phase)
0.5333	Remote Similarity	NPD4247	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