NPASS Compound

Natural Product: NPC602672

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 -4.5076 -2.3195 -1.1881 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7118 -1.2438 -0.1032 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8305 -1.8271 0.7793 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2548 -0.0547 -0.7797 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0785 1.1699 0.0165 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6325 1.4135 0.3658 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.7238 2.5169 1.4557 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9645 2.0718 -0.7749 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4572 2.1842 -0.7114 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8535 0.7721 -0.4668 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4317 -0.0141 -1.6249 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4720 0.4432 0.8351 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7232 0.3889 1.8987 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7384 0.6345 1.9400 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2826 0.1555 0.6407 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7978 0.1047 0.6131 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4877 1.3783 0.8971 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1904 -0.8248 1.7868 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6658 -1.2053 1.6974 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0637 -1.8469 0.4296 C 0 0 2 0 0 0 0 0 0 0 0 0 6.4559 -1.8865 0.3773 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5894 -1.0679 -0.7690 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5801 -2.0899 -1.9235 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5568 -0.0050 -1.1429 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1629 -0.6477 -0.6090 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5834 -0.1217 -1.8816 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0775 -0.1898 -1.7153 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6159 0.7253 -0.5536 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0930 2.0864 -0.9853 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9384 0.2241 0.9688 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4209 -1.1257 0.6202 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5402 -2.6310 -1.4834 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0492 -1.8946 -2.0926 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9864 -3.1958 -0.7888 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1723 -1.0963 1.5243 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3869 -2.6998 1.2751 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6553 -2.1813 0.1282 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3724 -0.2012 -0.9019 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8950 0.0010 -1.8250 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4322 2.0765 -0.5246 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6203 1.0491 0.9786 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7401 2.7256 1.8768 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4781 2.1887 2.2019 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0994 3.4549 0.9921 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2563 1.7363 -1.7898 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2999 3.1604 -0.7994 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2404 2.8748 0.0950 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1472 2.6118 -1.6648 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5224 -0.1053 -1.6198 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9596 -0.9612 -1.8438 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2510 0.6496 -2.5267 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2049 0.1392 2.8639 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1787 0.0225 2.7795 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9929 1.6789 2.1981 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0030 -0.9521 0.6165 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1730 1.7630 0.1246 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1577 1.3586 1.8157 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7136 2.1342 1.2218 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1731 -0.2054 2.7350 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5761 -1.7185 1.8308 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3187 -0.3345 1.9050 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8310 -1.9185 2.5291 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6631 -2.8906 0.3996 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8629 -1.1323 0.9067 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6431 -2.6846 -1.8416 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7287 -1.6114 -2.8898 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4182 -2.8191 -1.7711 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3867 -0.5011 -1.7329 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1603 0.7644 -1.8133 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1168 0.4235 -0.2591 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6210 -1.6465 -0.4769 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9826 0.7918 -2.2785 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8029 -0.9149 -2.6613 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6363 0.0534 -2.6642 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9113 -1.2501 -1.3550 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7636 2.1778 -2.0669 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1891 2.1862 -1.0936 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6988 2.9016 -0.3521 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2009 0.3095 2.0796 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5544 -1.8076 1.5291 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5790 -1.6782 0.1196 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 1 6 8 1 0 8 9 1 0 9 10 1 0 10 11 1 6 10 12 1 0 12 13 2 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 1 16 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 20 22 1 0 22 23 1 0 22 24 1 0 22 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 6 12 30 1 0 30 31 1 0 31 2 1 0 30 6 1 0 28 10 1 0 28 15 1 0 25 16 1 0 1 32 1 0 1 33 1 0 1 34 1 0 3 35 1 0 3 36 1 0 3 37 1 0 4 38 1 0 4 39 1 0 5 40 1 0 5 41 1 0 7 42 1 0 7 43 1 0 7 44 1 0 8 45 1 0 8 46 1 0 9 47 1 0 9 48 1 0 11 49 1 0 11 50 1 0 11 51 1 0 13 52 1 0 14 53 1 0 14 54 1 0 15 55 1 1 17 56 1 0 17 57 1 0 17 58 1 0 18 59 1 0 18 60 1 0 19 61 1 0 19 62 1 0 20 63 1 6 21 64 1 0 23 65 1 0 23 66 1 0 23 67 1 0 24 68 1 0 24 69 1 0 24 70 1 0 25 71 1 1 26 72 1 0 26 73 1 0 27 74 1 0 27 75 1 0 29 76 1 0 29 77 1 0 29 78 1 0 30 79 1 1 31 80 1 0 31 81 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 NPC602672 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	25597
0.1-0.2	19934
0.2-0.3	3118
0.3-0.4	855
0.4-0.5	232
0.5-0.6	63
0.6-0.7	34
0.7-0.8	0
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC290598
1.0	High Similarity	NPC30590
0.8269	Intermediate Similarity	NPC101475
0.8269	Intermediate Similarity	NPC196753
0.8113	Intermediate Similarity	NPC235341
0.7679	Intermediate Similarity	NPC246708
0.7636	Intermediate Similarity	NPC470588
0.7593	Intermediate Similarity	NPC34177
0.7455	Intermediate Similarity	NPC253807
0.7455	Intermediate Similarity	NPC158662
0.7407	Intermediate Similarity	NPC474989
0.7358	Intermediate Similarity	NPC27765
0.7358	Intermediate Similarity	NPC122418
0.7358	Intermediate Similarity	NPC491014
0.7037	Intermediate Similarity	NPC601696
0.6964	Remote Similarity	NPC311078
0.6842	Remote Similarity	NPC475862
0.6721	Remote Similarity	NPC171203
0.6721	Remote Similarity	NPC307426
0.6721	Remote Similarity	NPC98442
0.6721	Remote Similarity	NPC488519
0.6721	Remote Similarity	NPC242468
0.6552	Remote Similarity	NPC478657
0.6552	Remote Similarity	NPC480924
0.6316	Remote Similarity	NPC142754
0.629	Remote Similarity	NPC172361
0.6271	Remote Similarity	NPC40394
0.6271	Remote Similarity	NPC195334
0.619	Remote Similarity	NPC7260
0.619	Remote Similarity	NPC210037
0.619	Remote Similarity	NPC120968
0.619	Remote Similarity	NPC227467
0.619	Remote Similarity	NPC273621
0.6167	Remote Similarity	NPC230295
0.6167	Remote Similarity	NPC53744
0.6167	Remote Similarity	NPC159168
0.6167	Remote Similarity	NPC95594
0.6167	Remote Similarity	NPC98386
0.614	Remote Similarity	NPC120098
0.6066	Remote Similarity	NPC480950
0.6056	Remote Similarity	NPC167383
0.6032	Remote Similarity	NPC480946
0.6032	Remote Similarity	NPC130577
0.6032	Remote Similarity	NPC142415
0.6032	Remote Similarity	NPC102683
0.6032	Remote Similarity	NPC610937
0.6	Remote Similarity	NPC49776
0.6	Remote Similarity	NPC63118
0.6	Remote Similarity	NPC474436
0.5968	Remote Similarity	NPC40552
0.5902	Remote Similarity	NPC238992
0.5873	Remote Similarity	NPC477579
0.5833	Remote Similarity	NPC132478
0.5821	Remote Similarity	NPC294360
0.5781	Remote Similarity	NPC213412
0.5781	Remote Similarity	NPC10005
0.5781	Remote Similarity	NPC91525
0.5781	Remote Similarity	NPC136313
0.5781	Remote Similarity	NPC2539
0.5738	Remote Similarity	NPC291379
0.5714	Remote Similarity	NPC231431
0.5692	Remote Similarity	NPC112866
0.5672	Remote Similarity	NPC263393
0.5625	Remote Similarity	NPC477872
0.5606	Remote Similarity	NPC18872
0.5606	Remote Similarity	NPC290614
0.5574	Remote Similarity	NPC237344
0.5556	Remote Similarity	NPC133954
0.5538	Remote Similarity	NPC187722
0.5538	Remote Similarity	NPC191965
0.5522	Remote Similarity	NPC228784
0.5522	Remote Similarity	NPC324341
0.5522	Remote Similarity	NPC164349
0.5522	Remote Similarity	NPC601810
0.55	Remote Similarity	NPC474488
0.5484	Remote Similarity	NPC471899
0.5455	Remote Similarity	NPC182797
0.5455	Remote Similarity	NPC51700
0.5455	Remote Similarity	NPC88716
0.5455	Remote Similarity	NPC68160
0.5455	Remote Similarity	NPC52169
0.5455	Remote Similarity	NPC488562
0.5455	Remote Similarity	NPC606443
0.5439	Remote Similarity	NPC472805
0.5439	Remote Similarity	NPC90979
0.5397	Remote Similarity	NPC224145
0.5397	Remote Similarity	NPC3915
0.5385	Remote Similarity	NPC17733
0.5385	Remote Similarity	NPC137306
0.5385	Remote Similarity	NPC470629
0.5303	Remote Similarity	NPC214756
0.5303	Remote Similarity	NPC198664
0.5303	Remote Similarity	NPC295643
0.5294	Remote Similarity	NPC202728
0.5294	Remote Similarity	NPC158059
0.5294	Remote Similarity	NPC293564
0.5263	Remote Similarity	NPC237503
0.5224	Remote Similarity	NPC195019
0.5217	Remote Similarity	NPC480919
0.5172	Remote Similarity	NPC138374
0.5172	Remote Similarity	NPC34700
0.5156	Remote Similarity	NPC253402
0.5152	Remote Similarity	NPC162107
0.5152	Remote Similarity	NPC46912
0.5147	Remote Similarity	NPC23621
0.5139	Remote Similarity	NPC471433
0.5139	Remote Similarity	NPC283343
0.5139	Remote Similarity	NPC471432
0.5077	Remote Similarity	NPC267517
0.5072	Remote Similarity	NPC29765
0.507	Remote Similarity	NPC488520
0.5068	Remote Similarity	NPC473160

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC602672 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8013
0.1-0.2	1066
0.2-0.3	66
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
0.5938	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