NPASS Compound

Natural Product: NPC601652

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 87 92 0 0 0 0 0 0 0 0999 V2000 -11.3036 -0.8929 1.5924 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.4847 0.1848 1.9538 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.2294 0.4164 1.4467 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5998 -0.3805 0.5107 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3400 -0.1034 0.0349 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6486 0.9992 0.4831 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2723 1.8153 1.4304 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5377 1.5269 1.9008 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.0782 2.3986 2.8445 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3090 1.2790 -0.0352 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2041 0.8071 0.9041 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8769 1.1226 0.3170 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3032 2.3442 0.6121 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0735 2.7046 0.1009 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4073 1.7990 -0.7334 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8412 2.1479 -1.2611 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9333 0.5715 -1.0582 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2976 -0.3401 -1.8779 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9367 -0.9139 -1.6661 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0851 -2.0145 -0.8190 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3058 -2.5671 -0.6222 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4669 -2.0939 -1.2307 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7303 -2.8127 -0.9657 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3106 -2.4667 0.3259 C 0 0 2 0 0 0 0 0 0 0 0 0 5.7522 -1.1124 0.6405 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0387 -0.1286 -0.2725 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4530 1.1249 0.1970 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7474 2.1374 -0.7026 O 0 0 0 0 0 0 0 0 0 0 0 0 6.6332 1.9163 -2.0754 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5683 1.3531 1.5511 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9755 2.5895 1.9812 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1486 3.0029 3.3004 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2778 0.3480 2.4772 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8778 -0.8628 2.0235 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5807 -2.0559 2.8654 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2218 -3.3152 2.3326 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2927 -3.3779 0.8844 N 0 0 0 0 0 0 0 0 0 0 0 0 7.6283 -3.0810 0.4792 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3125 -1.0178 -2.0589 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0489 -0.4323 -2.2728 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1777 0.2832 -0.5023 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0439 0.8394 -1.3637 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.7382 1.9070 -2.2933 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0091 -0.0281 -1.9539 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6804 -0.9686 -0.9699 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.7739 -1.7902 1.2559 H 0 0 0 0 0 0 0 0 0 0 0 0 -12.0541 -1.1340 2.3884 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.9268 -0.5450 0.7193 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.1450 -1.2472 0.1587 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7093 2.6760 1.7677 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.7416 3.0814 2.4947 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2020 2.4048 -0.0434 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2343 -0.2974 1.0328 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3362 1.2604 1.9039 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7992 3.0544 1.2512 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6243 3.6588 0.3314 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6163 2.2480 -0.6061 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1699 -2.3775 -0.3479 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3996 -3.4134 0.0326 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4956 -3.9024 -0.9851 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3797 -2.6111 -1.8505 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4116 -2.6440 1.0693 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9854 -0.2933 -1.3395 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1764 1.0293 -2.4353 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0498 2.8014 -2.6355 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5626 1.7597 -2.3952 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3212 2.2186 4.0402 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0508 3.6697 3.3255 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3156 3.6443 3.6737 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3599 0.5006 3.5456 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0251 -1.8779 3.8930 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5050 -2.2469 3.0112 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6673 -4.1928 2.7165 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2472 -3.3705 2.7562 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1360 -2.3162 1.1029 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2402 -4.0214 0.6100 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7357 -2.8259 -0.5917 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1705 -0.6084 -2.5876 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0061 0.4083 -2.9482 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6087 -0.6794 -0.7464 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9637 2.9048 -1.8346 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6448 1.9249 -2.5420 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2840 1.8409 -3.2416 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8485 0.5537 -2.4341 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4927 -0.6528 -2.7125 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3876 -1.5827 -1.5382 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9364 -1.6620 -0.5113 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 2 0 8 9 1 0 6 10 1 0 10 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 15 17 1 0 17 18 1 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 2 0 26 27 1 0 27 28 1 0 28 29 1 0 27 30 2 0 30 31 1 0 31 32 1 0 30 33 1 0 33 34 2 0 34 35 1 0 35 36 1 0 36 37 1 0 37 38 1 0 22 39 1 0 39 40 2 0 17 41 2 0 10 42 1 0 42 43 1 0 42 44 1 0 44 45 1 0 8 3 1 0 41 12 1 0 45 5 1 0 40 19 1 0 37 24 1 0 34 25 1 0 1 46 1 0 1 47 1 0 1 48 1 0 4 49 1 0 7 50 1 0 9 51 1 0 10 52 1 6 11 53 1 0 11 54 1 0 13 55 1 0 14 56 1 0 16 57 1 0 20 58 1 0 21 59 1 0 23 60 1 0 23 61 1 0 24 62 1 1 26 63 1 0 29 64 1 0 29 65 1 0 29 66 1 0 32 67 1 0 32 68 1 0 32 69 1 0 33 70 1 0 35 71 1 0 35 72 1 0 36 73 1 0 36 74 1 0 38 75 1 0 38 76 1 0 38 77 1 0 39 78 1 0 40 79 1 0 41 80 1 0 43 81 1 0 43 82 1 0 43 83 1 0 44 84 1 0 44 85 1 0 45 86 1 0 45 87 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 NPC601652 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	27301
0.1-0.2	20193
0.2-0.3	1937
0.3-0.4	247
0.4-0.5	80
0.5-0.6	45
0.6-0.7	36
0.7-0.8	0
0.8-0.85	1
0.85-0.9	2
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC240841
0.8889	High Similarity	NPC317272
0.8889	High Similarity	NPC268503
0.8116	Intermediate Similarity	NPC603603
0.7826	Intermediate Similarity	NPC480592
0.7746	Intermediate Similarity	NPC610959
0.7429	Intermediate Similarity	NPC256012
0.7429	Intermediate Similarity	NPC610965
0.7273	Intermediate Similarity	NPC181796
0.7273	Intermediate Similarity	NPC54654
0.7273	Intermediate Similarity	NPC7715
0.7273	Intermediate Similarity	NPC328155
0.7273	Intermediate Similarity	NPC222661
0.7273	Intermediate Similarity	NPC285931
0.7051	Intermediate Similarity	NPC290005
0.7013	Intermediate Similarity	NPC185639
0.7013	Intermediate Similarity	NPC251735
0.7013	Intermediate Similarity	NPC49075
0.7013	Intermediate Similarity	NPC599951
0.6923	Remote Similarity	NPC274716
0.6923	Remote Similarity	NPC167116
0.6923	Remote Similarity	NPC609821
0.6883	Remote Similarity	NPC286119
0.6875	Remote Similarity	NPC601489
0.6875	Remote Similarity	NPC604804
0.6818	Remote Similarity	NPC135538
0.6818	Remote Similarity	NPC24233
0.6818	Remote Similarity	NPC321505
0.6818	Remote Similarity	NPC179825
0.6795	Remote Similarity	NPC223690
0.6795	Remote Similarity	NPC9532
0.679	Remote Similarity	NPC611658
0.6753	Remote Similarity	NPC608819
0.6667	Remote Similarity	NPC212237
0.6667	Remote Similarity	NPC147390
0.6667	Remote Similarity	NPC428
0.6585	Remote Similarity	NPC24260
0.6585	Remote Similarity	NPC8836
0.6522	Remote Similarity	NPC247639
0.6522	Remote Similarity	NPC25084
0.6375	Remote Similarity	NPC601503
0.6364	Remote Similarity	NPC185838
0.625	Remote Similarity	NPC600054
0.625	Remote Similarity	NPC600872
0.625	Remote Similarity	NPC601504
0.6176	Remote Similarity	NPC191376
0.6049	Remote Similarity	NPC311973
0.6049	Remote Similarity	NPC239824
0.6	Remote Similarity	NPC290582
0.6	Remote Similarity	NPC217748
0.6	Remote Similarity	NPC182052
0.6	Remote Similarity	NPC271013
0.6	Remote Similarity	NPC42663
0.6	Remote Similarity	NPC15414
0.6	Remote Similarity	NPC314682
0.5976	Remote Similarity	NPC254441
0.5926	Remote Similarity	NPC279228
0.5909	Remote Similarity	NPC213206
0.5909	Remote Similarity	NPC188163
0.5909	Remote Similarity	NPC328750
0.5889	Remote Similarity	NPC41122
0.5889	Remote Similarity	NPC318805
0.5824	Remote Similarity	NPC60295
0.5761	Remote Similarity	NPC201508
0.5616	Remote Similarity	NPC104196
0.5595	Remote Similarity	NPC116465
0.5591	Remote Similarity	NPC175890
0.5584	Remote Similarity	NPC30779
0.5542	Remote Similarity	NPC609914
0.55	Remote Similarity	NPC276890
0.5455	Remote Similarity	NPC605743
0.5444	Remote Similarity	NPC480590
0.5385	Remote Similarity	NPC206900
0.5375	Remote Similarity	NPC76682
0.5375	Remote Similarity	NPC10908
0.5375	Remote Similarity	NPC63646
0.5375	Remote Similarity	NPC317145
0.5375	Remote Similarity	NPC198498
0.5375	Remote Similarity	NPC115284
0.5349	Remote Similarity	NPC229373
0.5319	Remote Similarity	NPC191132
0.5275	Remote Similarity	NPC480586
0.5213	Remote Similarity	NPC85381
0.5205	Remote Similarity	NPC317439
0.5181	Remote Similarity	NPC12424
0.5181	Remote Similarity	NPC129518
0.5181	Remote Similarity	NPC251580
0.5147	Remote Similarity	NPC34559
0.5119	Remote Similarity	NPC480591
0.5119	Remote Similarity	NPC603853
0.5116	Remote Similarity	NPC475393
0.5116	Remote Similarity	NPC112248
0.5111	Remote Similarity	NPC275680
0.5111	Remote Similarity	NPC22115
0.506	Remote Similarity	NPC227060
0.5059	Remote Similarity	NPC73492
0.5059	Remote Similarity	NPC299990
0.5059	Remote Similarity	NPC480587
0.5054	Remote Similarity	NPC82457
0.5054	Remote Similarity	NPC473589

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC601652 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4325
0.1-0.2	4648
0.2-0.3	158
0.3-0.4	12
0.4-0.5	0
0.5-0.6	7
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
0.5934	Remote Similarity	NPD8054	Phase 4
0.5909	Remote Similarity	NPD4664	Clinical (unspecified phase)
0.5652	Remote Similarity	NPD8053	Approved
0.5541	Remote Similarity	NPD4010	Discontinued
0.5375	Remote Similarity	NPD8099	Discontinued
0.5119	Remote Similarity	NPD8156	Discontinued
0.5059	Remote Similarity	NPD8095	Phase 1

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