NPASS Compound

Natural Product: NPC601313

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 104108 0 0 0 0 0 0 0 0999 V2000 -5.9179 -0.9712 -2.7543 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5416 -0.4587 -2.8565 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1263 0.0218 -3.9232 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7107 -0.5147 -1.7584 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3685 0.0038 -1.9250 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6426 -0.1647 -0.5999 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4733 0.6358 0.3764 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.8680 0.6247 0.0681 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8006 0.0938 0.9059 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2331 0.1237 0.5154 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4281 -0.4114 1.9959 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1111 2.1072 0.3591 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9137 2.8117 1.2504 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8922 3.7169 0.9108 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6573 4.3807 1.9964 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0873 3.9344 -0.3028 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6546 2.3786 0.4048 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1319 1.8085 -0.9376 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2095 2.1955 -1.1507 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5863 2.8836 -2.3133 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9822 3.3117 -2.5845 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6553 3.1208 -3.1270 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2271 0.3597 -0.6253 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2519 0.3226 0.7097 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1370 1.5065 1.3257 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5688 1.2493 2.6651 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4027 2.2427 1.6901 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5755 1.7703 1.1608 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8357 2.1762 1.3342 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0637 3.1457 2.1000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9713 1.5686 0.6830 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5416 2.3948 -0.3191 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6184 2.0328 -1.0674 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1645 0.7945 -0.8182 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6255 0.0329 0.1196 N 0 0 0 0 0 0 0 0 0 0 0 0 5.5274 0.3745 0.8996 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1475 -0.6461 1.9034 C 0 0 1 0 0 0 0 0 0 0 0 0 5.6201 -0.1067 3.2558 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7245 -1.0078 2.0250 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6509 -2.1926 3.0221 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0650 -1.3450 0.7527 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6774 -1.5341 -0.3248 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6982 -1.4603 0.7117 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9050 -1.7617 -0.4210 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3949 -2.2418 0.1710 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4542 -3.6457 -0.1102 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4950 -4.6341 0.8302 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5546 -6.0472 0.3978 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4799 -4.3028 2.0467 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6375 -1.6194 -0.2925 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1395 -2.4310 -1.3679 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2749 -3.1902 -1.2995 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6570 -3.9774 -2.5140 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9402 -3.1971 -0.2396 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7346 -0.5453 -1.3124 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5148 -0.8780 -2.7462 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9662 0.1162 -1.2929 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0339 -1.5852 -1.8489 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0585 -1.6678 -3.6316 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6767 -0.1614 -2.7980 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4040 1.0220 -2.2987 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0223 -0.7515 -2.6920 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3885 0.1495 1.3474 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3695 0.6762 -0.4244 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8559 0.5897 1.3245 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5817 -0.9169 0.3857 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4512 2.4526 -0.6695 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8083 5.4474 1.6717 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6388 3.9103 2.1521 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0871 4.4408 2.9367 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4693 3.4418 0.5019 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7983 2.0930 -1.7495 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0172 3.6792 -3.6304 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3141 4.1196 -1.9173 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6511 2.4279 -2.5147 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0634 1.6303 3.5315 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6166 0.1598 2.9022 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4971 1.7973 2.7850 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5677 2.3111 2.8078 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3306 3.3371 1.4020 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0430 3.3745 -0.4333 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0428 2.6738 -1.8300 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0332 0.4318 -1.3816 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7280 -1.5893 1.7734 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8773 -0.9408 3.9319 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8633 0.5374 3.7072 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5574 0.4800 3.0826 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1775 -0.2193 2.5597 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3779 -2.9615 2.7085 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9826 -1.7790 3.9955 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6299 -2.5533 3.1383 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4255 -2.5528 -0.9889 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3929 -2.2151 1.3051 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7892 -6.6640 1.2670 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2982 -6.1189 -0.4003 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4556 -6.2819 -0.0355 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4109 -1.7784 0.5229 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7422 -4.1707 -2.5678 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0750 -4.9254 -2.4667 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2817 -3.4448 -3.4143 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1188 -0.0571 -3.3510 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0470 -1.8717 -2.9069 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5209 -1.0611 -3.2669 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4528 0.1293 -2.1263 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 1 0 6 5 1 6 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 9 11 2 0 7 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 14 16 2 0 12 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 20 22 2 0 18 23 1 0 23 24 1 1 24 25 1 0 25 26 1 1 25 27 1 0 27 28 1 0 28 29 1 0 29 30 2 0 29 31 1 0 31 32 2 0 32 33 1 0 33 34 2 0 34 35 1 0 35 36 2 0 36 37 1 0 37 38 1 0 37 39 1 0 39 40 1 0 39 41 1 0 41 42 2 0 41 43 1 0 43 44 1 0 44 45 1 0 45 46 1 0 46 47 1 0 47 48 1 0 47 49 2 0 45 50 1 0 50 51 1 0 51 52 1 0 52 53 1 0 52 54 2 0 44 55 1 0 55 56 1 0 55 57 1 6 23 6 1 0 36 31 1 0 50 6 1 0 25 17 1 0 55 23 1 0 1 58 1 0 1 59 1 0 1 60 1 0 5 61 1 0 5 62 1 0 7 63 1 1 10 64 1 0 10 65 1 0 10 66 1 0 12 67 1 6 15 68 1 0 15 69 1 0 15 70 1 0 17 71 1 1 18 72 1 6 21 73 1 0 21 74 1 0 21 75 1 0 26 76 1 0 26 77 1 0 26 78 1 0 27 79 1 0 27 80 1 0 32 81 1 0 33 82 1 0 34 83 1 0 37 84 1 6 38 85 1 0 38 86 1 0 38 87 1 0 39 88 1 1 40 89 1 0 40 90 1 0 40 91 1 0 44 92 1 6 45 93 1 1 48 94 1 0 48 95 1 0 48 96 1 0 50 97 1 1 53 98 1 0 53 99 1 0 53100 1 0 56101 1 0 56102 1 0 56103 1 0 57104 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 NPC601313 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	22682
0.1-0.2	26321
0.2-0.3	694
0.3-0.4	79
0.4-0.5	7
0.5-0.6	22
0.6-0.7	22
0.7-0.8	0
0.8-0.85	5
0.85-0.9	7
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC76565
0.8876	High Similarity	NPC326930
0.8791	High Similarity	NPC476110
0.8778	High Similarity	NPC475301
0.8681	High Similarity	NPC87152
0.8681	High Similarity	NPC475600
0.8681	High Similarity	NPC475631
0.8571	High Similarity	NPC475303
0.8387	Intermediate Similarity	NPC475596
0.809	Intermediate Similarity	NPC35208
0.8061	Intermediate Similarity	NPC483853
0.8061	Intermediate Similarity	NPC608314
0.8022	Intermediate Similarity	NPC475498
0.79	Intermediate Similarity	NPC475426
0.7889	Intermediate Similarity	NPC250807
0.7889	Intermediate Similarity	NPC57797
0.7778	Intermediate Similarity	NPC328928
0.77	Intermediate Similarity	NPC327769
0.7609	Intermediate Similarity	NPC475137
0.7551	Intermediate Similarity	NPC475644
0.7524	Intermediate Similarity	NPC483856
0.7368	Intermediate Similarity	NPC146824
0.7358	Intermediate Similarity	NPC483854
0.729	Intermediate Similarity	NPC482915
0.72	Intermediate Similarity	NPC30456
0.72	Intermediate Similarity	NPC488904
0.7188	Intermediate Similarity	NPC473833
0.7041	Intermediate Similarity	NPC53255
0.7041	Intermediate Similarity	NPC85879
0.7021	Intermediate Similarity	NPC470306
0.699	Remote Similarity	NPC477787
0.69	Remote Similarity	NPC122968
0.69	Remote Similarity	NPC328186
0.69	Remote Similarity	NPC228377
0.6893	Remote Similarity	NPC244839
0.6893	Remote Similarity	NPC600583
0.6832	Remote Similarity	NPC470486
0.6667	Remote Similarity	NPC319880
0.6667	Remote Similarity	NPC316841
0.6667	Remote Similarity	NPC320324
0.6667	Remote Similarity	NPC471977
0.6602	Remote Similarity	NPC13603
0.6569	Remote Similarity	NPC475533
0.6476	Remote Similarity	NPC473689
0.6476	Remote Similarity	NPC292416
0.6449	Remote Similarity	NPC327904
0.6449	Remote Similarity	NPC38959
0.6389	Remote Similarity	NPC471979
0.6364	Remote Similarity	NPC471016
0.6262	Remote Similarity	NPC475406
0.6132	Remote Similarity	NPC471190
0.6058	Remote Similarity	NPC475362
0.5981	Remote Similarity	NPC324619
0.5941	Remote Similarity	NPC473850
0.5888	Remote Similarity	NPC475315
0.5856	Remote Similarity	NPC170751
0.5833	Remote Similarity	NPC600224
0.5763	Remote Similarity	NPC483855
0.5727	Remote Similarity	NPC611166
0.5688	Remote Similarity	NPC604935
0.566	Remote Similarity	NPC473506
0.5596	Remote Similarity	NPC328154
0.5586	Remote Similarity	NPC600607
0.5577	Remote Similarity	NPC471014
0.5536	Remote Similarity	NPC601643
0.5455	Remote Similarity	NPC477788
0.5398	Remote Similarity	NPC253482
0.5333	Remote Similarity	NPC475408
0.5263	Remote Similarity	NPC237702
0.5225	Remote Similarity	NPC607403
0.521	Remote Similarity	NPC469748
0.5138	Remote Similarity	NPC483892
0.513	Remote Similarity	NPC475648
0.5091	Remote Similarity	NPC475601

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC601313 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4816
0.1-0.2	4311
0.2-0.3	23
0.3-0.4	0
0.4-0.5	0
0.5-0.6	0
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
		NPD

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