NPASS Compound

Natural Product: NPC607723

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 81 85 0 0 0 0 0 0 0 0999 V2000 2.3554 1.7284 2.7019 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0990 1.3263 1.4184 C 0 0 1 0 0 0 0 0 0 0 0 0 4.5817 1.4715 1.7935 C 0 0 2 0 0 0 0 0 0 0 0 0 4.8855 2.9222 2.1062 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3144 1.1644 0.4777 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2157 -0.3195 0.3078 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8219 -0.8613 0.3266 C 0 0 2 0 0 0 0 0 0 0 0 0 3.9765 -2.2768 0.9265 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3970 -1.0954 -1.0976 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9796 -1.5830 -1.2279 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0027 -0.5551 -0.6122 C 0 0 2 0 0 0 0 0 0 0 0 0 1.2092 0.7093 -1.4109 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4624 -0.4535 0.7813 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6126 -0.6794 1.7535 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8119 -1.0395 1.5853 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2315 -0.3963 0.2922 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7029 -0.3211 0.1490 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4443 -1.5718 0.5460 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1850 0.7704 1.1184 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8255 1.9222 0.3892 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9806 1.4275 -0.4333 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9268 0.8606 0.4076 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4649 0.4992 -1.4854 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3737 -0.6636 -1.6835 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4785 1.2944 -2.8027 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0409 0.1553 -1.2278 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4807 -0.8500 -2.1964 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9578 -0.6406 -2.1684 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4157 -1.0120 -0.7910 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4868 -2.5244 -0.8149 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8488 -0.1165 1.1803 C 0 0 2 0 0 0 0 0 0 0 0 0 1.2773 1.7390 2.5288 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5730 0.9806 3.4910 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7409 2.7263 3.0463 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9111 2.0487 0.6615 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8851 0.7763 2.5728 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7398 3.1662 3.1744 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2181 3.5824 1.5075 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9585 3.1111 1.8743 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7950 1.6887 -0.3511 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3816 1.4264 0.5556 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7267 -0.6486 -0.6303 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8458 -0.7676 1.1324 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5804 -2.9210 0.2815 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0205 -2.7214 1.1751 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5554 -2.1096 1.8708 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6741 -0.2808 -1.7949 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0307 -1.9651 -1.4604 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9121 -2.4695 -0.5636 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7683 -1.7703 -2.2755 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1411 0.3937 -2.4970 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4540 1.4784 -1.2729 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2529 1.0911 -1.3830 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9196 -0.6145 2.8231 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4409 -0.7253 2.4432 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8488 -2.1470 1.5786 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8732 0.6779 0.3725 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8440 -2.0994 1.3129 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7443 -2.2068 -0.2830 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4012 -1.3185 1.0944 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3440 1.2030 1.7070 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9115 0.3997 1.8490 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2746 2.5686 1.1983 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1244 2.5634 -0.1477 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4712 2.3485 -0.8666 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6190 1.5174 0.6948 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8784 -1.0246 -0.7694 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2171 -0.3159 -2.3517 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8858 -1.4822 -2.2651 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4650 0.5525 -3.6002 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4470 1.8299 -2.8595 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6017 1.9344 -2.9038 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4438 1.0968 -1.3907 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7846 -1.8765 -2.0502 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7856 -0.5471 -3.2300 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8535 0.4324 -2.4076 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6018 -1.3281 -2.9622 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0420 -3.0272 -0.0183 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5118 -2.8855 -0.8301 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0258 -2.8393 -1.7912 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0399 -0.5337 2.2313 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 3 5 1 0 5 6 1 0 6 7 1 0 7 8 1 1 7 9 1 0 9 10 1 0 10 11 1 0 11 12 1 6 11 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 1 17 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 21 23 1 0 23 24 1 0 23 25 1 0 23 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 1 13 31 1 0 31 2 1 0 31 7 1 0 29 11 1 0 29 16 1 0 26 17 1 0 1 32 1 0 1 33 1 0 1 34 1 0 2 35 1 6 3 36 1 1 4 37 1 0 4 38 1 0 4 39 1 0 5 40 1 0 5 41 1 0 6 42 1 0 6 43 1 0 8 44 1 0 8 45 1 0 8 46 1 0 9 47 1 0 9 48 1 0 10 49 1 0 10 50 1 0 12 51 1 0 12 52 1 0 12 53 1 0 14 54 1 0 15 55 1 0 15 56 1 0 16 57 1 1 18 58 1 0 18 59 1 0 18 60 1 0 19 61 1 0 19 62 1 0 20 63 1 0 20 64 1 0 21 65 1 6 22 66 1 0 24 67 1 0 24 68 1 0 24 69 1 0 25 70 1 0 25 71 1 0 25 72 1 0 26 73 1 6 27 74 1 0 27 75 1 0 28 76 1 0 28 77 1 0 30 78 1 0 30 79 1 0 30 80 1 0 31 81 1 1 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 NPC607723 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	26363
0.1-0.2	19472
0.2-0.3	2999
0.3-0.4	735
0.4-0.5	188
0.5-0.6	70
0.6-0.7	19
0.7-0.8	0
0.8-0.85	1
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	NPC27765
1.0	High Similarity	NPC122418
1.0	High Similarity	NPC491014
0.8113	Intermediate Similarity	NPC40394
0.7963	Intermediate Similarity	NPC95594
0.7679	Intermediate Similarity	NPC40552
0.7593	Intermediate Similarity	NPC132478
0.7544	Intermediate Similarity	NPC477579
0.7358	Intermediate Similarity	NPC290598
0.7358	Intermediate Similarity	NPC30590
0.7037	Intermediate Similarity	NPC120098
0.6833	Remote Similarity	NPC610937
0.6724	Remote Similarity	NPC602872
0.6552	Remote Similarity	NPC291379
0.6379	Remote Similarity	NPC101475
0.6316	Remote Similarity	NPC82477
0.629	Remote Similarity	NPC86372
0.6271	Remote Similarity	NPC235341
0.6271	Remote Similarity	NPC290495
0.619	Remote Similarity	NPC51700
0.619	Remote Similarity	NPC171203
0.619	Remote Similarity	NPC88716
0.619	Remote Similarity	NPC307426
0.619	Remote Similarity	NPC98442
0.619	Remote Similarity	NPC68160
0.619	Remote Similarity	NPC242468
0.6182	Remote Similarity	NPC469770
0.6102	Remote Similarity	NPC196753
0.6094	Remote Similarity	NPC18872
0.6094	Remote Similarity	NPC290614
0.5968	Remote Similarity	NPC246708
0.5968	Remote Similarity	NPC610552
0.5938	Remote Similarity	NPC307335
0.5938	Remote Similarity	NPC74855
0.5938	Remote Similarity	NPC195019
0.5902	Remote Similarity	NPC470588
0.5833	Remote Similarity	NPC311078
0.5833	Remote Similarity	NPC34177
0.5781	Remote Similarity	NPC329943
0.5758	Remote Similarity	NPC49776
0.5758	Remote Similarity	NPC63118
0.5758	Remote Similarity	NPC474436
0.5738	Remote Similarity	NPC253807
0.5738	Remote Similarity	NPC158662
0.5692	Remote Similarity	NPC7260
0.5692	Remote Similarity	NPC210037
0.5692	Remote Similarity	NPC120968
0.5692	Remote Similarity	NPC227467
0.5692	Remote Similarity	NPC273621
0.5692	Remote Similarity	NPC112866
0.5667	Remote Similarity	NPC474989
0.5645	Remote Similarity	NPC292015
0.5645	Remote Similarity	NPC159168
0.5625	Remote Similarity	NPC477872
0.5556	Remote Similarity	NPC480950
0.5538	Remote Similarity	NPC480946
0.5538	Remote Similarity	NPC187722
0.5538	Remote Similarity	NPC274330
0.5538	Remote Similarity	NPC130577
0.5538	Remote Similarity	NPC142415
0.5538	Remote Similarity	NPC102683
0.5538	Remote Similarity	NPC473242
0.5538	Remote Similarity	NPC290690
0.5522	Remote Similarity	NPC98874
0.5484	Remote Similarity	NPC471897
0.5455	Remote Similarity	NPC182797
0.5455	Remote Similarity	NPC488519
0.5455	Remote Similarity	NPC52169
0.5455	Remote Similarity	NPC488562
0.5455	Remote Similarity	NPC606443
0.5443	Remote Similarity	NPC477292
0.541	Remote Similarity	NPC295131
0.5397	Remote Similarity	NPC107039
0.5385	Remote Similarity	NPC479748
0.5323	Remote Similarity	NPC237344
0.5303	Remote Similarity	NPC272075
0.5303	Remote Similarity	NPC304285
0.5303	Remote Similarity	NPC2539
0.5294	Remote Similarity	NPC202728
0.5294	Remote Similarity	NPC158059
0.5294	Remote Similarity	NPC293564
0.5238	Remote Similarity	NPC480924
0.5231	Remote Similarity	NPC606009
0.5217	Remote Similarity	NPC263393
0.5172	Remote Similarity	NPC472805
0.5172	Remote Similarity	NPC90979
0.5156	Remote Similarity	NPC230295
0.5156	Remote Similarity	NPC238992
0.5156	Remote Similarity	NPC98386
0.5152	Remote Similarity	NPC127855
0.5147	Remote Similarity	NPC61543
0.5147	Remote Similarity	NPC293048
0.5147	Remote Similarity	NPC225585
0.5147	Remote Similarity	NPC184006
0.5082	Remote Similarity	NPC601696
0.5072	Remote Similarity	NPC228784
0.5072	Remote Similarity	NPC324341
0.5072	Remote Similarity	NPC164349
0.5072	Remote Similarity	NPC601810
0.5068	Remote Similarity	NPC171208

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC607723 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8040
0.1-0.2	1060
0.2-0.3	45
0.3-0.4	3
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
0.5224	Remote Similarity	NPD7645	Phase 2

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