NPASS Compound

Natural Product: NPC601771

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 34 36 0 0 0 0 0 0 0 0999 V2000 5.3845 0.9041 1.9855 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2336 0.5147 1.3131 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5704 1.4573 0.5790 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4077 1.1110 -0.1143 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9022 -0.1625 -0.0823 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6665 -0.5903 -0.8099 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2011 -1.2973 0.0104 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4845 -0.8468 0.2535 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1849 -1.0661 1.4159 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4653 -0.6070 1.6337 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1545 -0.8432 2.8229 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0730 0.1178 0.6128 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4202 0.3744 -0.5860 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0121 1.0947 -1.6122 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1614 -0.1069 -0.7335 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3588 0.1243 -1.9936 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0095 0.5776 -1.4579 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7950 1.0411 -2.5088 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5780 -1.1074 0.6613 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7441 -0.7744 1.3610 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3096 0.7051 1.6270 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9415 2.4711 0.5318 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8962 1.8594 -0.6808 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9520 -1.2750 -1.6633 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7070 -1.6358 2.2183 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1327 -1.1504 2.7668 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0659 0.4857 0.7551 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3167 0.5835 -2.4440 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8258 0.8709 -2.6351 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1904 -0.8615 -2.4804 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1505 1.3727 -0.7207 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0267 0.2946 -3.1171 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2336 -2.1353 0.7309 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2727 -1.5003 1.9387 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 2 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 1 0 10 12 2 0 12 13 1 0 13 14 1 0 13 15 2 0 15 16 1 0 16 17 1 0 17 18 1 0 5 19 1 0 19 20 2 0 20 2 1 0 17 6 1 0 15 8 1 0 1 21 1 0 3 22 1 0 4 23 1 0 6 24 1 6 9 25 1 0 11 26 1 0 12 27 1 0 14 28 1 0 16 29 1 0 16 30 1 0 17 31 1 1 18 32 1 0 19 33 1 0 20 34 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 NPC601771 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	23835
0.1-0.2	20670
0.2-0.3	4596
0.3-0.4	545
0.4-0.5	125
0.5-0.6	50
0.6-0.7	10
0.7-0.8	0
0.8-0.85	6
0.85-0.9	0
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC207179
1.0	High Similarity	NPC167571
1.0	High Similarity	NPC278552
0.8222	Intermediate Similarity	NPC261619
0.8222	Intermediate Similarity	NPC61477
0.8222	Intermediate Similarity	NPC78770
0.8222	Intermediate Similarity	NPC219876
0.8222	Intermediate Similarity	NPC126029
0.8222	Intermediate Similarity	NPC15658
0.74	Intermediate Similarity	NPC16435
0.74	Intermediate Similarity	NPC171932
0.7391	Intermediate Similarity	NPC268266
0.7391	Intermediate Similarity	NPC42760
0.7391	Intermediate Similarity	NPC220825
0.7391	Intermediate Similarity	NPC268342
0.7083	Intermediate Similarity	NPC47398
0.7083	Intermediate Similarity	NPC234333
0.7083	Intermediate Similarity	NPC260898
0.7	Intermediate Similarity	NPC61946
0.6458	Remote Similarity	NPC482472
0.6379	Remote Similarity	NPC277331
0.6379	Remote Similarity	NPC100482
0.6102	Remote Similarity	NPC601999
0.6078	Remote Similarity	NPC62290
0.6078	Remote Similarity	NPC142731
0.6078	Remote Similarity	NPC326506
0.6066	Remote Similarity	NPC308402
0.6066	Remote Similarity	NPC28440
0.6032	Remote Similarity	NPC211561
0.5833	Remote Similarity	NPC58190
0.5833	Remote Similarity	NPC108811
0.5833	Remote Similarity	NPC9636
0.5833	Remote Similarity	NPC170103
0.5833	Remote Similarity	NPC236202
0.5833	Remote Similarity	NPC262911
0.5833	Remote Similarity	NPC202742
0.58	Remote Similarity	NPC601844
0.5738	Remote Similarity	NPC246202
0.5738	Remote Similarity	NPC224161
0.5738	Remote Similarity	NPC46335
0.5738	Remote Similarity	NPC294558
0.5738	Remote Similarity	NPC18185
0.5738	Remote Similarity	NPC263940
0.5738	Remote Similarity	NPC279406
0.5738	Remote Similarity	NPC486519
0.5714	Remote Similarity	NPC155564
0.5625	Remote Similarity	NPC70409
0.5625	Remote Similarity	NPC204770
0.5625	Remote Similarity	NPC600551
0.5625	Remote Similarity	NPC601980
0.5625	Remote Similarity	NPC602065
0.5625	Remote Similarity	NPC611024
0.5574	Remote Similarity	NPC607430
0.5538	Remote Similarity	NPC601997
0.5538	Remote Similarity	NPC609211
0.5538	Remote Similarity	NPC610665
0.5455	Remote Similarity	NPC186228
0.5373	Remote Similarity	NPC134911
0.5323	Remote Similarity	NPC82917
0.5312	Remote Similarity	NPC313116
0.5312	Remote Similarity	NPC603340
0.5303	Remote Similarity	NPC226809
0.5246	Remote Similarity	NPC96576
0.5192	Remote Similarity	NPC1940
0.5179	Remote Similarity	NPC36835
0.5179	Remote Similarity	NPC246162
0.5179	Remote Similarity	NPC9743
0.5179	Remote Similarity	NPC260491
0.5179	Remote Similarity	NPC61506
0.5179	Remote Similarity	NPC240476
0.5152	Remote Similarity	NPC470802
0.5147	Remote Similarity	NPC46283
0.5147	Remote Similarity	NPC469944
0.5147	Remote Similarity	NPC278548
0.5143	Remote Similarity	NPC306267
0.5091	Remote Similarity	NPC103799
0.5085	Remote Similarity	NPC150670
0.5085	Remote Similarity	NPC482704
0.5082	Remote Similarity	NPC156818

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC601771 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4483
0.1-0.2	4469
0.2-0.3	183
0.3-0.4	9
0.4-0.5	3
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8222	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.8222	Intermediate 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