NPASS Compound

Natural Product: NPC607774

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 44 46 0 0 0 0 0 0 0 0999 V2000 -5.2435 -0.4627 1.5635 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3265 0.0304 0.1697 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3663 1.0206 -0.1977 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4806 -0.4103 -0.7341 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4419 -1.4007 -0.3645 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0664 -0.9439 -0.5707 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2669 -0.5437 0.4925 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0245 -0.1121 0.3146 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5578 -0.0712 -0.9693 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2577 -0.4746 -2.0123 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5552 -0.9101 -1.8503 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3035 -1.2979 -2.9634 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8430 0.3603 -1.1255 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6806 0.9519 -0.1900 C 0 0 2 0 0 0 0 0 0 0 0 0 3.9504 0.2059 -0.0183 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9948 -1.1792 0.0975 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1925 -1.8516 0.2582 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3726 -1.1385 0.3055 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5969 -1.7727 0.4655 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3388 0.2233 0.1926 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1351 0.8714 0.0333 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0410 1.2478 1.1472 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8881 0.3159 1.4007 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6546 -0.1054 2.5519 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2224 -0.2289 1.9666 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4019 -1.5601 1.5437 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0257 0.0110 2.2139 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9967 2.0696 -0.0387 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6429 0.8423 -1.2534 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2834 0.8678 0.4094 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5760 -0.0212 -1.7502 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6211 -2.3659 -0.9226 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5667 -1.6660 0.6994 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6335 -0.5547 1.5259 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1527 -0.4447 -3.0122 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3084 -0.7785 -3.8309 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9584 1.9626 -0.6114 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0488 -1.6970 0.0553 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2117 -2.9366 0.3475 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1637 -1.6308 1.3060 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2627 0.8051 0.2278 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1676 1.9655 -0.0520 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6136 2.2711 1.1916 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7377 1.1452 1.9879 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 2 3 4 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 11 12 1 0 9 13 1 0 13 14 1 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 18 20 1 0 20 21 2 0 14 22 1 0 22 23 1 0 23 24 2 0 11 6 1 0 21 15 1 0 23 8 1 0 1 25 1 0 1 26 1 0 1 27 1 0 3 28 1 0 3 29 1 0 3 30 1 0 4 31 1 0 5 32 1 0 5 33 1 0 7 34 1 0 10 35 1 0 12 36 1 0 14 37 1 6 16 38 1 0 17 39 1 0 19 40 1 0 20 41 1 0 21 42 1 0 22 43 1 0 22 44 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 NPC607774 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	18067
0.1-0.2	25926
0.2-0.3	4906
0.3-0.4	660
0.4-0.5	217
0.5-0.6	53
0.6-0.7	16
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	Natural Product ID
1.0	High Similarity	NPC39329
1.0	High Similarity	NPC51032
0.7719	Intermediate Similarity	NPC221432
0.7719	Intermediate Similarity	NPC257097
0.7368	Intermediate Similarity	NPC169591
0.7368	Intermediate Similarity	NPC298223
0.7368	Intermediate Similarity	NPC604412
0.7069	Intermediate Similarity	NPC143896
0.6833	Remote Similarity	NPC75049
0.65	Remote Similarity	NPC164980
0.6452	Remote Similarity	NPC109223
0.6452	Remote Similarity	NPC68104
0.6452	Remote Similarity	NPC220998
0.6452	Remote Similarity	NPC10937
0.6349	Remote Similarity	NPC125855
0.6349	Remote Similarity	NPC76338
0.6349	Remote Similarity	NPC250242
0.6308	Remote Similarity	NPC291508
0.6296	Remote Similarity	NPC329225
0.6296	Remote Similarity	NPC147686
0.619	Remote Similarity	NPC197252
0.6129	Remote Similarity	NPC150408
0.6032	Remote Similarity	NPC69674
0.6032	Remote Similarity	NPC171651
0.5873	Remote Similarity	NPC107572
0.5873	Remote Similarity	NPC32739
0.5797	Remote Similarity	NPC228504
0.5714	Remote Similarity	NPC258630
0.5694	Remote Similarity	NPC209040
0.5694	Remote Similarity	NPC110303
0.5694	Remote Similarity	NPC601247
0.5652	Remote Similarity	NPC39752
0.5625	Remote Similarity	NPC1089
0.5625	Remote Similarity	NPC236766
0.5625	Remote Similarity	NPC472580
0.5593	Remote Similarity	NPC1612
0.5593	Remote Similarity	NPC183959
0.5556	Remote Similarity	NPC197351
0.5556	Remote Similarity	NPC185276
0.5538	Remote Similarity	NPC265040
0.5517	Remote Similarity	NPC476480
0.5517	Remote Similarity	NPC84585
0.5507	Remote Similarity	NPC36275
0.55	Remote Similarity	NPC324386
0.5455	Remote Similarity	NPC66515
0.5455	Remote Similarity	NPC310130
0.5424	Remote Similarity	NPC32441
0.5424	Remote Similarity	NPC79943
0.5417	Remote Similarity	NPC488556
0.541	Remote Similarity	NPC469764
0.5385	Remote Similarity	NPC245482
0.5373	Remote Similarity	NPC223500
0.5373	Remote Similarity	NPC106976
0.5342	Remote Similarity	NPC472627
0.5303	Remote Similarity	NPC149026
0.5294	Remote Similarity	NPC608140
0.5286	Remote Similarity	NPC35038
0.5278	Remote Similarity	NPC472629
0.5254	Remote Similarity	NPC225153
0.5254	Remote Similarity	NPC479876
0.5246	Remote Similarity	NPC300668
0.5246	Remote Similarity	NPC329203
0.5246	Remote Similarity	NPC222342
0.5231	Remote Similarity	NPC482704
0.5224	Remote Similarity	NPC17170
0.5205	Remote Similarity	NPC479215
0.52	Remote Similarity	NPC472628
0.5167	Remote Similarity	NPC264083
0.5161	Remote Similarity	NPC210084
0.5152	Remote Similarity	NPC91560
0.5147	Remote Similarity	NPC166689
0.5143	Remote Similarity	NPC470890
0.5143	Remote Similarity	NPC200761
0.5143	Remote Similarity	NPC473078
0.5139	Remote Similarity	NPC479211
0.5068	Remote Similarity	NPC485619
0.5068	Remote Similarity	NPC479213

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC607774 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3315
0.1-0.2	5655
0.2-0.3	170
0.3-0.4	6
0.4-0.5	2
0.5-0.6	1
0.6-0.7	1
0.7-0.8	0
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
0.6296	Remote Similarity	NPD1549	Phase 2
0.5424	Remote Similarity	NPD1552	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