NPASS Compound

Natural Product: NPC611680

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 35 37 0 0 0 0 0 0 0 0999 V2000 4.0122 1.1642 3.0480 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4613 0.6909 1.8562 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1359 -0.1843 1.0255 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5928 -0.6522 -0.1514 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2990 -1.5418 -0.9791 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3390 -0.2477 -0.5313 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6301 0.6214 0.2619 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2062 1.0685 1.4328 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3384 1.0486 -0.1133 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4274 0.3690 -1.0948 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8029 0.2901 -0.5775 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4988 -0.8917 -0.6541 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8019 -1.0073 -0.1773 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3846 0.1194 0.3846 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6908 -0.0142 0.8573 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6831 1.3082 0.4612 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3203 2.4062 1.0359 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3740 1.4154 -0.0206 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2067 -0.9486 -1.3662 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2852 -1.6747 -0.1787 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6642 -0.6970 -1.7837 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1902 2.1535 3.0997 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1420 -0.5190 1.3145 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1911 -2.5502 -0.7879 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6595 1.7560 2.0717 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3684 1.0411 -2.0014 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0208 -1.7394 -1.0916 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3151 -1.9552 -0.2564 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9212 -0.8044 1.4798 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1022 3.3151 0.6535 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8256 2.3503 0.0409 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3288 -1.4895 -2.1721 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7082 -2.5440 -0.4167 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0681 -1.6888 -2.0719 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7360 0.0320 -2.5975 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 1 0 4 6 2 0 6 7 1 0 7 8 2 0 7 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 14 16 1 0 16 17 1 0 16 18 2 0 10 19 1 0 19 20 1 0 19 21 1 0 8 2 1 0 18 11 1 0 21 6 1 0 1 22 1 0 3 23 1 0 5 24 1 0 8 25 1 0 10 26 1 6 12 27 1 0 13 28 1 0 15 29 1 0 17 30 1 0 18 31 1 0 19 32 1 6 20 33 1 0 21 34 1 0 21 35 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 NPC611680 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	20564
0.1-0.2	23294
0.2-0.3	5335
0.3-0.4	453
0.4-0.5	94
0.5-0.6	64
0.6-0.7	28
0.7-0.8	0
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	6

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC261619
1.0	High Similarity	NPC61477
1.0	High Similarity	NPC78770
1.0	High Similarity	NPC219876
1.0	High Similarity	NPC126029
1.0	High Similarity	NPC15658
0.8222	Intermediate Similarity	NPC207179
0.8222	Intermediate Similarity	NPC167571
0.8222	Intermediate Similarity	NPC278552
0.7826	Intermediate Similarity	NPC268266
0.7826	Intermediate Similarity	NPC42760
0.7826	Intermediate Similarity	NPC220825
0.7826	Intermediate Similarity	NPC268342
0.7241	Intermediate Similarity	NPC28440
0.7115	Intermediate Similarity	NPC16435
0.7115	Intermediate Similarity	NPC171932
0.7018	Intermediate Similarity	NPC58190
0.7018	Intermediate Similarity	NPC108811
0.7018	Intermediate Similarity	NPC170103
0.7018	Intermediate Similarity	NPC236202
0.7018	Intermediate Similarity	NPC262911
0.7018	Intermediate Similarity	NPC202742
0.6897	Remote Similarity	NPC246202
0.6897	Remote Similarity	NPC224161
0.6897	Remote Similarity	NPC46335
0.6897	Remote Similarity	NPC294558
0.6897	Remote Similarity	NPC18185
0.6897	Remote Similarity	NPC263940
0.6897	Remote Similarity	NPC279406
0.6897	Remote Similarity	NPC486519
0.6875	Remote Similarity	NPC601844
0.68	Remote Similarity	NPC47398
0.68	Remote Similarity	NPC234333
0.68	Remote Similarity	NPC260898
0.6731	Remote Similarity	NPC61946
0.6415	Remote Similarity	NPC36835
0.6415	Remote Similarity	NPC246162
0.6415	Remote Similarity	NPC9743
0.6415	Remote Similarity	NPC260491
0.6415	Remote Similarity	NPC61506
0.6415	Remote Similarity	NPC240476
0.6349	Remote Similarity	NPC226809
0.625	Remote Similarity	NPC150670
0.6182	Remote Similarity	NPC178054
0.6167	Remote Similarity	NPC82917
0.6167	Remote Similarity	NPC9636
0.6154	Remote Similarity	NPC278548
0.6129	Remote Similarity	NPC313116
0.6129	Remote Similarity	NPC308402
0.6129	Remote Similarity	NPC603340
0.5938	Remote Similarity	NPC70409
0.5938	Remote Similarity	NPC204770
0.5938	Remote Similarity	NPC600551
0.5938	Remote Similarity	NPC601980
0.5938	Remote Similarity	NPC602065
0.5938	Remote Similarity	NPC611024
0.5909	Remote Similarity	NPC302549
0.5902	Remote Similarity	NPC469313
0.5758	Remote Similarity	NPC272552
0.5758	Remote Similarity	NPC226108
0.5758	Remote Similarity	NPC322899
0.5758	Remote Similarity	NPC600630
0.5758	Remote Similarity	NPC607896
0.5758	Remote Similarity	NPC611369
0.5738	Remote Similarity	NPC289990
0.5735	Remote Similarity	NPC20050
0.5692	Remote Similarity	NPC470802
0.5672	Remote Similarity	NPC46283
0.5672	Remote Similarity	NPC469944
0.5652	Remote Similarity	NPC306267
0.5645	Remote Similarity	NPC607430
0.5588	Remote Similarity	NPC44192
0.5577	Remote Similarity	NPC482472
0.5574	Remote Similarity	NPC96576
0.5571	Remote Similarity	NPC135021
0.5556	Remote Similarity	NPC20757
0.5556	Remote Similarity	NPC227516
0.5469	Remote Similarity	NPC184245
0.5469	Remote Similarity	NPC187801
0.5469	Remote Similarity	NPC610920
0.5455	Remote Similarity	NPC246328
0.5455	Remote Similarity	NPC27532
0.5429	Remote Similarity	NPC478616
0.5429	Remote Similarity	NPC478339
0.541	Remote Similarity	NPC474656
0.541	Remote Similarity	NPC38779
0.541	Remote Similarity	NPC114179
0.541	Remote Similarity	NPC68324
0.541	Remote Similarity	NPC289322
0.541	Remote Similarity	NPC160512
0.5405	Remote Similarity	NPC86630
0.5397	Remote Similarity	NPC277331
0.5397	Remote Similarity	NPC100482
0.5342	Remote Similarity	NPC147743
0.5342	Remote Similarity	NPC4809
0.5342	Remote Similarity	NPC73517
0.5333	Remote Similarity	NPC106601
0.5333	Remote Similarity	NPC151474
0.5333	Remote Similarity	NPC478340
0.5263	Remote Similarity	NPC212614
0.5263	Remote Similarity	NPC205613
0.5217	Remote Similarity	NPC134911
0.5156	Remote Similarity	NPC601196
0.5156	Remote Similarity	NPC601999
0.5147	Remote Similarity	NPC211561
0.5147	Remote Similarity	NPC601997
0.5147	Remote Similarity	NPC609211
0.5147	Remote Similarity	NPC610665
0.5132	Remote Similarity	NPC78074
0.5088	Remote Similarity	NPC321011
0.5088	Remote Similarity	NPC294852
0.5088	Remote Similarity	NPC188679
0.5085	Remote Similarity	NPC471744
0.5063	Remote Similarity	NPC159526

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC611680 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3797
0.1-0.2	5162
0.2-0.3	178
0.3-0.4	8
0.4-0.5	3
0.5-0.6	0
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	2

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD1612	Clinical (unspecified phase)
1.0	High Similarity	NPD1613	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