NPASS Compound

Natural Product: NPC607453

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 82 86 0 0 0 0 0 0 0 0999 V2000 -5.4909 1.2661 -2.5773 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6652 0.0834 -2.1494 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2909 -0.7098 -3.3731 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4263 -0.7060 -1.1401 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1303 -0.2409 0.2694 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7078 -0.6332 0.6587 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.8045 -2.1237 1.0092 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5442 -2.5740 1.3800 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2097 0.1457 1.8150 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7401 0.1128 2.0629 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8860 0.2601 0.8374 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9074 1.7319 0.4756 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4644 -0.5777 -0.2407 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7325 -1.4429 -0.9264 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7233 -1.6776 -0.7039 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2264 -0.3427 -0.2004 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7089 -0.3391 -0.2937 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3930 -1.6271 0.0437 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0357 -0.0776 -1.7752 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4739 0.1241 -2.0565 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2201 1.0232 -1.1399 C 0 0 2 0 0 0 0 0 0 0 0 0 6.5524 0.5402 -1.0774 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7230 1.0975 0.2586 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5916 0.2711 1.1997 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9339 2.5506 0.7365 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2648 0.8567 0.4112 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7846 0.8418 1.8126 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2820 1.1478 1.7253 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5808 -0.0621 1.0971 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7331 -1.1482 2.1296 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8900 -0.5358 -0.6026 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3861 0.5831 -1.4302 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0179 1.8562 -3.3854 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4939 0.8781 -2.8642 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6704 1.8999 -1.6669 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0454 -1.4607 -3.6291 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2567 -1.1279 -3.2973 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2455 0.0059 -4.2346 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5218 -0.5211 -1.3199 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3041 -1.7932 -1.2306 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3348 0.8300 0.3902 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8251 -0.7979 0.9664 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1867 -2.7247 0.1849 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4943 -2.2657 1.8674 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5494 -3.5490 1.5296 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8165 -0.1468 2.6965 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4976 1.2188 1.6453 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5103 -0.8481 2.5671 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5026 0.9016 2.8090 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2365 2.0193 -0.3290 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8956 2.1352 0.2304 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6845 2.3033 1.4368 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1816 -2.0395 -1.7105 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2257 -2.0472 -1.5936 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7419 -2.4494 0.1229 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8587 0.4489 -0.9222 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2508 -1.8479 -0.6623 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8666 -1.6506 1.0438 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7518 -2.5274 -0.0431 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5062 0.8934 -2.0034 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6370 -0.8453 -2.4329 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5131 0.6058 -3.0849 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0346 -0.8424 -2.2429 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3465 2.0556 -1.5866 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1208 1.1734 -0.5657 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0047 -0.6356 0.6814 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5204 0.8690 1.4489 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1173 0.0624 2.1556 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0482 2.5863 1.8250 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0712 3.1372 0.3583 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8270 2.9668 0.1956 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7609 1.7464 -0.0844 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2165 1.7514 2.3255 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0284 -0.0099 2.4240 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2626 2.0344 1.0462 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9644 1.3445 2.7456 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0593 -2.0059 1.9894 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5914 -0.7250 3.1696 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7470 -1.5585 2.1337 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1747 -1.4708 -1.1901 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8320 1.4267 -0.8229 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7465 0.9227 -2.2407 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 7 8 1 0 6 9 1 0 9 10 1 0 10 11 1 0 11 12 1 6 11 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 1 17 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 21 23 1 0 23 24 1 0 23 25 1 0 23 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 1 13 31 1 0 31 32 1 0 32 2 1 0 31 6 1 0 29 11 1 0 29 16 1 0 26 17 1 0 1 33 1 0 1 34 1 0 1 35 1 0 3 36 1 0 3 37 1 0 3 38 1 0 4 39 1 0 4 40 1 0 5 41 1 0 5 42 1 0 7 43 1 0 7 44 1 0 8 45 1 0 9 46 1 0 9 47 1 0 10 48 1 0 10 49 1 0 12 50 1 0 12 51 1 0 12 52 1 0 14 53 1 0 15 54 1 0 15 55 1 0 16 56 1 6 18 57 1 0 18 58 1 0 18 59 1 0 19 60 1 0 19 61 1 0 20 62 1 0 20 63 1 0 21 64 1 6 22 65 1 0 24 66 1 0 24 67 1 0 24 68 1 0 25 69 1 0 25 70 1 0 25 71 1 0 26 72 1 6 27 73 1 0 27 74 1 0 28 75 1 0 28 76 1 0 30 77 1 0 30 78 1 0 30 79 1 0 31 80 1 6 32 81 1 0 32 82 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 NPC607453 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	26083
0.1-0.2	19856
0.2-0.3	2731
0.3-0.4	878
0.4-0.5	213
0.5-0.6	64
0.6-0.7	22
0.7-0.8	0
0.8-0.85	2
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	NPC101475
0.8269	Intermediate Similarity	NPC290598
0.8269	Intermediate Similarity	NPC30590
0.7679	Intermediate Similarity	NPC235341
0.7679	Intermediate Similarity	NPC253807
0.7679	Intermediate Similarity	NPC158662
0.75	Intermediate Similarity	NPC311078
0.75	Intermediate Similarity	NPC196753
0.7288	Intermediate Similarity	NPC246708
0.7193	Intermediate Similarity	NPC34177
0.678	Remote Similarity	NPC40394
0.678	Remote Similarity	NPC480924
0.6667	Remote Similarity	NPC159168
0.6667	Remote Similarity	NPC3915
0.6508	Remote Similarity	NPC191965
0.6441	Remote Similarity	NPC474989
0.6406	Remote Similarity	NPC488519
0.6393	Remote Similarity	NPC230295
0.6393	Remote Similarity	NPC238992
0.6393	Remote Similarity	NPC470588
0.6393	Remote Similarity	NPC98386
0.6379	Remote Similarity	NPC27765
0.6379	Remote Similarity	NPC122418
0.6379	Remote Similarity	NPC491014
0.625	Remote Similarity	NPC167383
0.6066	Remote Similarity	NPC237344
0.6029	Remote Similarity	NPC294360
0.6	Remote Similarity	NPC480946
0.6	Remote Similarity	NPC213412
0.6	Remote Similarity	NPC130577
0.6	Remote Similarity	NPC142415
0.6	Remote Similarity	NPC102683
0.5968	Remote Similarity	NPC478657
0.5909	Remote Similarity	NPC7260
0.5909	Remote Similarity	NPC210037
0.5909	Remote Similarity	NPC120968
0.5909	Remote Similarity	NPC171203
0.5909	Remote Similarity	NPC307426
0.5909	Remote Similarity	NPC98442
0.5909	Remote Similarity	NPC242468
0.5909	Remote Similarity	NPC227467
0.5909	Remote Similarity	NPC273621
0.5873	Remote Similarity	NPC53744
0.5833	Remote Similarity	NPC120098
0.5833	Remote Similarity	NPC601696
0.5781	Remote Similarity	NPC480950
0.5735	Remote Similarity	NPC49776
0.5735	Remote Similarity	NPC63118
0.5735	Remote Similarity	NPC474436
0.5714	Remote Similarity	NPC475862
0.5679	Remote Similarity	NPC271494
0.5672	Remote Similarity	NPC182797
0.5672	Remote Similarity	NPC52169
0.5672	Remote Similarity	NPC488562
0.5658	Remote Similarity	NPC237503
0.5625	Remote Similarity	NPC253402
0.5625	Remote Similarity	NPC95594
0.5556	Remote Similarity	NPC283343
0.5522	Remote Similarity	NPC187722
0.5522	Remote Similarity	NPC198664
0.5522	Remote Similarity	NPC136313
0.5522	Remote Similarity	NPC2539
0.5522	Remote Similarity	NPC610937
0.5469	Remote Similarity	NPC291379
0.5455	Remote Similarity	NPC40552
0.5441	Remote Similarity	NPC51700
0.5441	Remote Similarity	NPC88716
0.5441	Remote Similarity	NPC68160
0.5441	Remote Similarity	NPC112866
0.5441	Remote Similarity	NPC606443
0.5429	Remote Similarity	NPC263393
0.5429	Remote Similarity	NPC480919
0.5373	Remote Similarity	NPC477872
0.5373	Remote Similarity	NPC477579
0.5362	Remote Similarity	NPC18872
0.5362	Remote Similarity	NPC290614
0.5312	Remote Similarity	NPC132478
0.5294	Remote Similarity	NPC172361
0.5286	Remote Similarity	NPC202728
0.5286	Remote Similarity	NPC158059
0.5286	Remote Similarity	NPC228784
0.5286	Remote Similarity	NPC324341
0.5286	Remote Similarity	NPC293564
0.5286	Remote Similarity	NPC164349
0.5286	Remote Similarity	NPC601810
0.527	Remote Similarity	NPC473160
0.5238	Remote Similarity	NPC142754
0.5231	Remote Similarity	NPC195334
0.5217	Remote Similarity	NPC270768
0.5217	Remote Similarity	NPC59263
0.5217	Remote Similarity	NPC210106
0.52	Remote Similarity	NPC480920
0.5135	Remote Similarity	NPC273668
0.5072	Remote Similarity	NPC274330
0.5072	Remote Similarity	NPC214756
0.5059	Remote Similarity	NPC29069

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC607453 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8045
0.1-0.2	1046
0.2-0.3	54
0.3-0.4	3
0.4-0.5	1
0.5-0.6	0
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
0.6154	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