NPASS Compound

Natural Product: NPC593428

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 91 0 0 0 0 0 0 0 0999 V2000 -1.2557 -5.4212 -0.0754 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8325 -4.2252 0.5832 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9164 -4.3533 1.2075 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2393 -2.9986 0.5399 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7428 -1.8200 1.1493 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7793 -1.2375 2.1429 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4521 0.2186 1.8808 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1846 0.7282 3.1856 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6223 0.3332 0.9271 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8917 -0.9797 0.3465 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9325 -1.7985 0.6341 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7320 -1.3845 1.5122 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2142 -3.0861 0.0368 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4933 -3.6636 -0.9831 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8374 -4.9158 -1.4874 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9159 -5.6083 -0.9718 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6446 -5.0545 0.0393 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2815 -3.8067 0.5241 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9646 1.4033 -0.0311 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4270 1.8568 0.0513 C 0 0 2 0 0 0 0 0 0 0 0 0 3.1381 1.5717 1.2139 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9408 2.0091 2.4815 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7890 1.6049 3.6470 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0035 2.7968 2.7227 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9604 3.1270 -0.4285 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1085 2.3788 -0.8545 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1094 1.5128 -1.2738 C 0 0 2 0 0 0 0 0 0 0 0 0 2.2300 1.9345 -2.3998 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8704 2.3807 -2.2233 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4827 3.5680 -2.8335 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2353 2.3736 -0.7857 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4210 3.8648 -0.3701 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2119 2.3370 -1.0688 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5329 3.0447 -2.2629 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9903 1.0580 -1.1424 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3539 1.5024 -1.3167 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0141 1.2798 -2.4822 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4341 1.7215 -2.7243 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4592 0.6857 -3.4247 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9306 0.4394 0.1610 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0109 -0.8767 -0.0204 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3587 -1.4780 -1.3251 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7974 0.8224 1.5805 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8254 2.2433 1.9844 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9779 0.2341 2.3128 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2624 -5.6085 0.3884 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9131 -6.2873 -0.0595 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0420 -5.1128 -1.1409 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6872 -2.1747 1.6163 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1300 -1.8640 2.0986 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0835 -1.4197 3.2017 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4378 0.0910 3.6398 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5245 0.3491 1.6399 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6509 -3.1367 -1.4043 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2858 -5.3831 -2.2839 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2147 -6.5854 -1.3383 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4964 -5.5833 0.4582 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9236 -3.4348 1.3397 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0971 0.6358 -0.9399 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5462 2.4009 3.7622 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1587 1.5603 4.5725 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2166 0.5979 3.5188 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3809 3.8540 0.3353 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6901 3.6780 -1.2863 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4592 0.4794 -1.2283 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8041 2.6989 -3.0118 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3195 1.0565 -3.1301 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2304 1.6076 -2.7751 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1585 3.9664 -3.3999 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5530 4.5342 -1.2100 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5924 4.2590 0.0226 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9988 3.9973 0.5294 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8156 2.9787 -0.3411 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5347 2.4872 -3.0547 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6814 0.5644 -2.0327 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6036 2.6037 -2.0808 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1534 0.9420 -2.4157 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5949 1.9523 -3.7966 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6664 -1.3506 -2.1440 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3508 -2.6154 -1.1782 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4487 -1.3366 -1.5910 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8935 2.1862 3.1354 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9278 2.8330 1.8793 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7909 2.7574 1.7669 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7715 -0.1285 1.5865 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6270 1.0371 2.8250 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7827 -0.4100 3.1478 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 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 2 0 11 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 9 19 1 0 19 20 1 0 20 21 1 1 21 22 1 0 22 23 1 0 22 24 2 0 20 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 29 31 1 0 31 32 1 1 31 33 1 0 33 34 1 0 33 35 1 0 35 36 1 0 36 37 1 0 37 38 1 0 37 39 2 0 35 40 1 0 40 41 2 0 41 42 1 0 40 43 1 0 43 44 1 0 43 45 1 0 41 5 1 0 43 7 1 0 18 13 1 0 31 19 1 0 27 20 1 0 1 46 1 0 1 47 1 0 1 48 1 0 5 49 1 1 6 50 1 0 6 51 1 0 8 52 1 0 9 53 1 1 14 54 1 0 15 55 1 0 16 56 1 0 17 57 1 0 18 58 1 0 19 59 1 6 23 60 1 0 23 61 1 0 23 62 1 0 25 63 1 0 25 64 1 0 27 65 1 1 28 66 1 0 28 67 1 0 29 68 1 6 30 69 1 0 32 70 1 0 32 71 1 0 32 72 1 0 33 73 1 1 34 74 1 0 35 75 1 6 38 76 1 0 38 77 1 0 38 78 1 0 42 79 1 0 42 80 1 0 42 81 1 0 44 82 1 0 44 83 1 0 44 84 1 0 45 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 NPC593428 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	8660
0.1-0.2	37767
0.2-0.3	2896
0.3-0.4	456
0.4-0.5	24
0.5-0.6	42
0.6-0.7	10
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	NPC605573
0.7922	Intermediate Similarity	NPC217918
0.764	Intermediate Similarity	NPC327699
0.6629	Remote Similarity	NPC603140
0.631	Remote Similarity	NPC609501
0.6267	Remote Similarity	NPC79303
0.6163	Remote Similarity	NPC155329
0.6163	Remote Similarity	NPC114357
0.6082	Remote Similarity	NPC36607
0.6023	Remote Similarity	NPC259144
0.6023	Remote Similarity	NPC219419
0.6	Remote Similarity	NPC471629
0.6	Remote Similarity	NPC306001
0.596	Remote Similarity	NPC471623
0.596	Remote Similarity	NPC208553
0.596	Remote Similarity	NPC181964
0.596	Remote Similarity	NPC307628
0.596	Remote Similarity	NPC473400
0.596	Remote Similarity	NPC603171
0.593	Remote Similarity	NPC197037
0.593	Remote Similarity	NPC229545
0.593	Remote Similarity	NPC248265
0.593	Remote Similarity	NPC134685
0.59	Remote Similarity	NPC33372
0.59	Remote Similarity	NPC67246
0.59	Remote Similarity	NPC324251
0.59	Remote Similarity	NPC206211
0.5842	Remote Similarity	NPC487360
0.5842	Remote Similarity	NPC479182
0.5842	Remote Similarity	NPC479180
0.5795	Remote Similarity	NPC11588
0.5758	Remote Similarity	NPC473300
0.5747	Remote Similarity	NPC91730
0.5743	Remote Similarity	NPC471754
0.5728	Remote Similarity	NPC471606
0.5728	Remote Similarity	NPC275170
0.57	Remote Similarity	NPC321072
0.57	Remote Similarity	NPC215892
0.57	Remote Similarity	NPC242662
0.57	Remote Similarity	NPC102167
0.57	Remote Similarity	NPC488127
0.5673	Remote Similarity	NPC486061
0.5673	Remote Similarity	NPC486060
0.5644	Remote Similarity	NPC453583
0.5644	Remote Similarity	NPC317882
0.5644	Remote Similarity	NPC191193
0.5619	Remote Similarity	NPC487361
0.5588	Remote Similarity	NPC479183
0.5588	Remote Similarity	NPC479181
0.5534	Remote Similarity	NPC478329
0.5444	Remote Similarity	NPC473632
0.5392	Remote Similarity	NPC473490
0.5192	Remote Similarity	NPC473558
0.5111	Remote Similarity	NPC38696
0.5096	Remote Similarity	NPC478328

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC593428 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3262
0.1-0.2	5686
0.2-0.3	189
0.3-0.4	0
0.4-0.5	3
0.5-0.6	10
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
0.596	Remote Similarity	NPD8485	Phase 4
0.57	Remote Similarity	NPD8360	Approved
0.57	Remote Similarity	NPD8361	Phase 4
0.5437	Remote Similarity	NPD8368	Phase 2
0.5392	Remote Similarity	NPD8424	Phase 3
0.534	Remote Similarity	NPD8435	Phase 4
0.5283	Remote Similarity	NPD8486	Phase 1
0.5185	Remote Similarity	NPD8470	Clinical (unspecified phase)
0.513	Remote Similarity	NPD8462	Phase 2
0.5093	Remote Similarity	NPD8434	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