NPASS Compound

Natural Product: NPC606657

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 80 84 0 0 0 0 0 0 0 0999 V2000 -7.3135 5.0874 0.2178 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9211 5.1900 0.4815 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0486 4.1386 0.3917 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3986 2.8694 0.0169 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4390 1.8433 -0.0500 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1361 2.0385 0.2465 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0614 1.0348 0.2408 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8216 1.5015 0.4152 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2463 0.7638 0.4401 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4988 1.2746 0.6212 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6750 0.4941 0.6528 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8768 1.1478 0.8459 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1039 0.4924 0.8953 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6848 0.5416 2.1525 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9521 0.0918 2.2878 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9386 -1.4284 2.3659 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9357 0.4824 1.2285 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2797 1.8223 1.2603 O 0 0 0 0 0 0 0 0 0 0 0 0 7.2995 0.1521 -0.1265 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2454 0.4715 -1.1294 O 0 0 0 0 0 0 0 0 0 0 0 0 8.7839 -0.5582 -1.9069 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7877 -0.2708 -2.9796 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3875 -1.7381 -1.6656 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0564 1.0026 -0.1830 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4381 2.2976 0.2001 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5084 -0.8528 0.4881 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2465 -1.3799 0.3041 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0594 -2.7654 0.1325 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1172 -0.5918 0.2782 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1030 -1.1382 0.0982 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1921 -2.3715 -0.0457 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2857 -0.3097 0.0720 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3948 -0.9533 -0.1026 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4745 -1.5589 -0.5282 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6075 -1.5325 0.2866 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7332 -1.6922 -0.4997 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9197 -2.0303 0.4234 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6215 -2.7139 -1.5827 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5133 -2.0583 -2.8258 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4711 -3.6552 -1.4542 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8767 -4.8523 -0.8437 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2586 -3.0742 -0.7867 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0351 -3.7204 0.4030 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7918 3.3367 0.6272 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7119 4.3495 0.6972 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3324 5.6405 1.0825 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5329 4.4045 -0.6071 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7947 4.6261 1.1227 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7972 6.0510 0.0701 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4169 2.6433 -0.2316 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7535 0.8937 -0.3697 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6168 2.3507 0.7490 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9643 -0.5737 0.6640 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4264 0.4069 3.2569 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5458 -1.7800 3.3401 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2694 -1.7886 1.5675 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9381 -1.8710 2.1497 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8817 -0.1066 1.3389 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1848 1.9034 0.8354 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0760 -0.9262 -0.0801 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3117 0.0224 -3.9259 H 0 0 0 0 0 0 0 0 0 0 0 0 10.4916 0.5268 -2.6655 H 0 0 0 0 0 0 0 0 0 0 0 0 10.4120 -1.1850 -3.1535 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5739 1.0667 -1.1559 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7520 2.7053 0.8009 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3469 -1.5096 0.5007 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2988 -3.3318 0.9379 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7851 -1.1871 -1.5454 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0021 -0.6781 -0.9113 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7913 -3.0866 0.7943 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.8379 -1.9097 -0.1838 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8646 -1.2928 1.2493 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5642 -3.3440 -1.5779 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1798 -2.7487 -3.4577 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1611 -3.9660 -2.4963 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0900 -5.2989 -0.4227 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3557 -3.1343 -1.4221 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3302 -4.3880 0.3636 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7774 3.5565 0.8745 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7149 6.1312 0.4475 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 2 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 15 17 1 0 17 18 1 0 17 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 21 23 2 0 19 24 1 0 24 25 1 0 11 26 2 0 26 27 1 0 27 28 1 0 27 29 2 0 29 30 1 0 30 31 2 0 30 32 1 0 32 33 1 0 33 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 36 38 1 0 38 39 1 0 38 40 1 0 40 41 1 0 40 42 1 0 42 43 1 0 6 44 1 0 44 45 2 0 45 46 1 0 45 3 1 0 32 7 2 0 42 34 1 0 29 9 1 0 24 13 1 0 1 47 1 0 1 48 1 0 1 49 1 0 4 50 1 0 5 51 1 0 10 52 1 0 13 53 1 0 15 54 1 0 16 55 1 0 16 56 1 0 16 57 1 0 17 58 1 0 18 59 1 0 19 60 1 0 22 61 1 0 22 62 1 0 22 63 1 0 24 64 1 0 25 65 1 0 26 66 1 0 28 67 1 0 34 68 1 0 36 69 1 0 37 70 1 0 37 71 1 0 37 72 1 0 38 73 1 0 39 74 1 0 40 75 1 0 41 76 1 0 42 77 1 0 43 78 1 0 44 79 1 0 46 80 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 NPC606657 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	17778
0.1-0.2	28853
0.2-0.3	2404
0.3-0.4	426
0.4-0.5	281
0.5-0.6	91
0.6-0.7	16
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.85	High Similarity	NPC611303
0.7386	Intermediate Similarity	NPC251417
0.7204	Intermediate Similarity	NPC483416
0.6977	Remote Similarity	NPC271692
0.6818	Remote Similarity	NPC219904
0.6782	Remote Similarity	NPC46420
0.6744	Remote Similarity	NPC249281
0.6667	Remote Similarity	NPC158674
0.6484	Remote Similarity	NPC605784
0.6413	Remote Similarity	NPC276377
0.6304	Remote Similarity	NPC116458
0.6304	Remote Similarity	NPC246943
0.62	Remote Similarity	NPC483413
0.618	Remote Similarity	NPC289667
0.6162	Remote Similarity	NPC72016
0.6082	Remote Similarity	NPC150164
0.602	Remote Similarity	NPC186816
0.6	Remote Similarity	NPC209296
0.6	Remote Similarity	NPC473327
0.5981	Remote Similarity	NPC470716
0.5934	Remote Similarity	NPC136042
0.5918	Remote Similarity	NPC293626
0.5914	Remote Similarity	NPC129217
0.59	Remote Similarity	NPC483414
0.59	Remote Similarity	NPC483415
0.587	Remote Similarity	NPC84362
0.587	Remote Similarity	NPC27640
0.5851	Remote Similarity	NPC22832
0.5851	Remote Similarity	NPC120099
0.5806	Remote Similarity	NPC59534
0.58	Remote Similarity	NPC64425
0.5773	Remote Similarity	NPC487212
0.5761	Remote Similarity	NPC297987
0.5761	Remote Similarity	NPC265530
0.5699	Remote Similarity	NPC305811
0.5686	Remote Similarity	NPC32641
0.5686	Remote Similarity	NPC256188
0.5686	Remote Similarity	NPC35119
0.5684	Remote Similarity	NPC21666
0.567	Remote Similarity	NPC265115
0.5625	Remote Similarity	NPC223747
0.5625	Remote Similarity	NPC470719
0.5625	Remote Similarity	NPC220169
0.561	Remote Similarity	NPC270620
0.5566	Remote Similarity	NPC14187
0.5532	Remote Similarity	NPC349108
0.5524	Remote Similarity	NPC101636
0.5521	Remote Similarity	NPC486578
0.5484	Remote Similarity	NPC127546
0.5484	Remote Similarity	NPC57625
0.5484	Remote Similarity	NPC19709
0.5484	Remote Similarity	NPC173637
0.5484	Remote Similarity	NPC317489
0.5484	Remote Similarity	NPC238376
0.5484	Remote Similarity	NPC223424
0.5484	Remote Similarity	NPC600591
0.5417	Remote Similarity	NPC60735
0.5417	Remote Similarity	NPC26230
0.5417	Remote Similarity	NPC285197
0.5408	Remote Similarity	NPC355481
0.5376	Remote Similarity	NPC111929
0.5376	Remote Similarity	NPC320283
0.5376	Remote Similarity	NPC473043
0.5376	Remote Similarity	NPC331652
0.5376	Remote Similarity	NPC41121
0.5368	Remote Similarity	NPC52550
0.5364	Remote Similarity	NPC480441
0.5361	Remote Similarity	NPC609478
0.534	Remote Similarity	NPC240306
0.5333	Remote Similarity	NPC142142
0.5333	Remote Similarity	NPC486577
0.5319	Remote Similarity	NPC108831
0.5319	Remote Similarity	NPC182634
0.531	Remote Similarity	NPC295625
0.5304	Remote Similarity	NPC470720
0.5294	Remote Similarity	NPC22062
0.5294	Remote Similarity	NPC473634
0.5294	Remote Similarity	NPC138811
0.5288	Remote Similarity	NPC470443
0.5248	Remote Similarity	NPC480466
0.5234	Remote Similarity	NPC470445
0.5229	Remote Similarity	NPC121703
0.5225	Remote Similarity	NPC25523
0.5217	Remote Similarity	NPC470717
0.5213	Remote Similarity	NPC135599
0.5213	Remote Similarity	NPC73855
0.5213	Remote Similarity	NPC113968
0.5213	Remote Similarity	NPC328940
0.5213	Remote Similarity	NPC277174
0.5213	Remote Similarity	NPC606877
0.5208	Remote Similarity	NPC181712
0.5179	Remote Similarity	NPC277532
0.5155	Remote Similarity	NPC472459
0.5152	Remote Similarity	NPC209023
0.5149	Remote Similarity	NPC278419
0.5149	Remote Similarity	NPC179198
0.514	Remote Similarity	NPC479765
0.514	Remote Similarity	NPC483412
0.5104	Remote Similarity	NPC95090
0.5104	Remote Similarity	NPC27408
0.5089	Remote Similarity	NPC470715
0.5089	Remote Similarity	NPC164704
0.5085	Remote Similarity	NPC175429
0.5053	Remote Similarity	NPC160515
0.5048	Remote Similarity	NPC126784
0.5048	Remote Similarity	NPC241423
0.5048	Remote Similarity	NPC153755
0.5047	Remote Similarity	NPC5319
0.5047	Remote Similarity	NPC488089
0.5043	Remote Similarity	NPC488086

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC606657 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5193
0.1-0.2	3910
0.2-0.3	38
0.3-0.4	3
0.4-0.5	2
0.5-0.6	3
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
0.6	Remote Similarity	NPD7054	Phase 4
0.5577	Remote Similarity	NPD7251	Phase 2
0.5514	Remote Similarity	NPD7808	Phase 3
0.5047	Remote Similarity	NPD7804	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