NPASS Compound

Natural Product: NPC602526

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 36 38 0 0 0 0 0 0 0 0999 V2000 -4.1805 3.3135 -0.7091 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5878 2.0647 -0.5262 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2888 1.0366 0.0695 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7290 -0.2089 0.2637 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4211 -1.2538 0.8615 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4330 -0.4474 -0.1442 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7181 0.5913 -0.7485 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2983 1.8339 -0.9341 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4173 0.3264 -1.1498 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2786 -0.8596 -0.8391 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6527 -0.4375 -0.4020 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7691 0.6198 0.4755 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9865 1.0573 0.9151 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0447 2.1131 1.7876 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1168 0.4027 0.4506 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3411 0.8554 0.9031 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9938 -0.6546 -0.4274 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1640 -1.2642 -0.8523 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7739 -1.0830 -0.8596 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3557 -1.5364 0.3530 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3052 -2.6724 0.7339 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8428 -1.7940 0.0722 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4987 3.8331 0.0990 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3160 1.2107 0.3976 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9108 -1.9688 0.3790 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7437 2.6293 -1.3996 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3333 -1.5556 -1.6943 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8616 1.1070 0.8169 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7883 3.0361 1.4670 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7928 1.6476 0.4729 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4773 -2.0704 -0.3146 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6860 -1.9131 -1.5483 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3466 -0.7852 1.1821 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9242 -2.4468 1.4751 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2455 -2.2793 0.9744 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9560 -2.4477 -0.8137 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 1 0 13 15 2 0 15 16 1 0 15 17 1 0 17 18 1 0 17 19 2 0 10 20 1 0 20 21 1 0 20 22 1 0 8 2 1 0 19 11 1 0 22 6 1 0 1 23 1 0 3 24 1 0 5 25 1 0 8 26 1 0 10 27 1 6 12 28 1 0 14 29 1 0 16 30 1 0 18 31 1 0 19 32 1 0 20 33 1 1 21 34 1 0 22 35 1 0 22 36 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 NPC602526 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	25465
0.1-0.2	21090
0.2-0.3	2935
0.3-0.4	206
0.4-0.5	90
0.5-0.6	48
0.6-0.7	8
0.7-0.8	2
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	4

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC268266
1.0	High Similarity	NPC42760
1.0	High Similarity	NPC220825
1.0	High Similarity	NPC268342
0.7826	Intermediate Similarity	NPC261619
0.7826	Intermediate Similarity	NPC61477
0.7826	Intermediate Similarity	NPC78770
0.7826	Intermediate Similarity	NPC219876
0.7826	Intermediate Similarity	NPC126029
0.7826	Intermediate Similarity	NPC15658
0.7447	Intermediate Similarity	NPC47398
0.7447	Intermediate Similarity	NPC234333
0.7447	Intermediate Similarity	NPC260898
0.7391	Intermediate Similarity	NPC207179
0.7391	Intermediate Similarity	NPC167571
0.7391	Intermediate Similarity	NPC278552
0.6909	Remote Similarity	NPC96576
0.6667	Remote Similarity	NPC9636
0.6667	Remote Similarity	NPC61946
0.6415	Remote Similarity	NPC16435
0.6415	Remote Similarity	NPC171932
0.6333	Remote Similarity	NPC308402
0.6275	Remote Similarity	NPC19721
0.6102	Remote Similarity	NPC607430
0.5806	Remote Similarity	NPC28440
0.5625	Remote Similarity	NPC470802
0.5574	Remote Similarity	NPC58190
0.5574	Remote Similarity	NPC108811
0.5574	Remote Similarity	NPC170103
0.5574	Remote Similarity	NPC236202
0.5574	Remote Similarity	NPC262911
0.5574	Remote Similarity	NPC202742
0.5538	Remote Similarity	NPC601997
0.5538	Remote Similarity	NPC609211
0.5538	Remote Similarity	NPC610665
0.5536	Remote Similarity	NPC291948
0.5536	Remote Similarity	NPC104983
0.5536	Remote Similarity	NPC250436
0.5536	Remote Similarity	NPC300845
0.5536	Remote Similarity	NPC88803
0.5484	Remote Similarity	NPC246202
0.5484	Remote Similarity	NPC224161
0.5484	Remote Similarity	NPC46335
0.5484	Remote Similarity	NPC294558
0.5484	Remote Similarity	NPC18185
0.5484	Remote Similarity	NPC263940
0.5484	Remote Similarity	NPC279406
0.5484	Remote Similarity	NPC486519
0.5455	Remote Similarity	NPC600630
0.5455	Remote Similarity	NPC607896
0.5455	Remote Similarity	NPC611369
0.527	Remote Similarity	NPC600812
0.5192	Remote Similarity	NPC482472
0.5192	Remote Similarity	NPC601844
0.5161	Remote Similarity	NPC289990
0.5161	Remote Similarity	NPC605048
0.5147	Remote Similarity	NPC65333
0.5147	Remote Similarity	NPC278548
0.5091	Remote Similarity	NPC325028
0.5091	Remote Similarity	NPC256346
0.5091	Remote Similarity	NPC606550
0.5082	Remote Similarity	NPC38779
0.5082	Remote Similarity	NPC114179
0.5082	Remote Similarity	NPC68324
0.5082	Remote Similarity	NPC289322
0.5082	Remote Similarity	NPC156818
0.5082	Remote Similarity	NPC160512
0.5079	Remote Similarity	NPC277331
0.5079	Remote Similarity	NPC100482
0.5075	Remote Similarity	NPC226809
0.5072	Remote Similarity	NPC44192
0.507	Remote Similarity	NPC135021

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC602526 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5398
0.1-0.2	3697
0.2-0.3	44
0.3-0.4	7
0.4-0.5	0
0.5-0.6	2
0.6-0.7	0
0.7-0.8	2
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
0.7826	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.7826	Intermediate Similarity	NPD1613	Phase 4
0.5536	Remote Similarity	NPD4868	Phase 3
0.5132	Remote Similarity	NPD7993	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