NPASS Compound

Natural Product: NPC605133

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 -5.2950 0.9696 1.0758 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8763 0.8245 1.1531 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2166 0.4032 0.0070 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8786 0.1291 -1.1706 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1342 -0.2835 -2.2540 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7726 -0.5735 -3.4751 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7696 -0.4133 -2.1472 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0818 -0.1421 -0.9690 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1972 -0.2643 -0.8710 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8600 -0.0042 0.2601 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3122 -0.1756 0.2628 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8975 -0.6017 -0.9286 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2490 -0.7811 -0.9925 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0378 -0.5455 0.1065 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4232 -0.7456 -0.0135 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5045 -0.1244 1.3013 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2770 0.1196 2.4221 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1065 0.0557 1.3494 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1850 0.4101 1.3769 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7547 0.7050 2.5872 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2156 0.5462 1.2768 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8555 0.9241 2.2856 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8443 0.2663 0.0931 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6882 -0.0219 0.7759 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5608 1.7123 0.2729 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7224 1.3579 2.0101 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9384 0.2476 -1.1942 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5897 -1.1937 -3.3712 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2114 -0.7387 -3.0130 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2490 -0.7811 -1.7843 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6755 -1.1144 -1.9370 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7002 -1.7340 -0.1170 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9381 0.9120 2.3903 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7285 0.3798 2.2822 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5551 0.2756 3.4650 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 1 0 5 7 2 0 7 8 1 0 8 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 2 0 19 20 1 0 19 21 1 0 21 22 2 0 21 23 1 0 23 3 1 0 23 8 2 0 18 11 1 0 1 24 1 0 1 25 1 0 1 26 1 0 4 27 1 0 6 28 1 0 7 29 1 0 12 30 1 0 13 31 1 0 15 32 1 0 17 33 1 0 18 34 1 0 20 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 NPC605133 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	26501
0.1-0.2	19420
0.2-0.3	2915
0.3-0.4	855
0.4-0.5	125
0.5-0.6	30
0.6-0.7	5
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC270465
0.7778	Intermediate Similarity	NPC604021
0.7407	Intermediate Similarity	NPC50728
0.7358	Intermediate Similarity	NPC149127
0.7222	Intermediate Similarity	NPC605047
0.6429	Remote Similarity	NPC87125
0.6324	Remote Similarity	NPC609879
0.625	Remote Similarity	NPC98661
0.625	Remote Similarity	NPC47815
0.6	Remote Similarity	NPC179271
0.5926	Remote Similarity	NPC51443
0.5862	Remote Similarity	NPC276905
0.5833	Remote Similarity	NPC236223
0.5818	Remote Similarity	NPC20791
0.5789	Remote Similarity	NPC230285
0.5763	Remote Similarity	NPC32420
0.569	Remote Similarity	NPC194281
0.5625	Remote Similarity	NPC216538
0.5593	Remote Similarity	NPC143799
0.5574	Remote Similarity	NPC261548
0.5574	Remote Similarity	NPC287101
0.5469	Remote Similarity	NPC259411
0.541	Remote Similarity	NPC470216
0.541	Remote Similarity	NPC55205
0.5357	Remote Similarity	NPC77858
0.5333	Remote Similarity	NPC286342
0.5333	Remote Similarity	NPC260895
0.5333	Remote Similarity	NPC281207
0.5333	Remote Similarity	NPC605755
0.5323	Remote Similarity	NPC602125
0.527	Remote Similarity	NPC599850
0.5246	Remote Similarity	NPC269652
0.5238	Remote Similarity	NPC133953
0.5238	Remote Similarity	NPC125062
0.5161	Remote Similarity	NPC54394
0.5082	Remote Similarity	NPC50403
0.5082	Remote Similarity	NPC7013
0.5082	Remote Similarity	NPC241838
0.5082	Remote Similarity	NPC188871
0.5079	Remote Similarity	NPC75215

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC605133 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5148
0.1-0.2	3922
0.2-0.3	73
0.3-0.4	5
0.4-0.5	1
0.5-0.6	1
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	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.5818	Remote Similarity	NPD1512	Phase 3

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