NPASS Compound

Natural Product: NPC600858

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 75 78 0 0 0 0 0 0 0 0999 V2000 6.8685 -0.8954 0.1311 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8429 0.5572 0.4929 C 0 0 1 0 0 0 0 0 0 0 0 0 8.1554 1.1759 -0.0387 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1634 2.5212 0.2800 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6693 1.2803 -0.0235 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3087 0.8850 0.4054 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8246 -0.4713 0.0930 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4020 -0.7561 0.5710 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4212 -0.5991 2.0691 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3841 0.0846 -0.1068 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4002 -0.1445 -1.6176 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1643 -1.0536 -1.7776 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7636 -0.2051 -0.9638 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1381 -0.6562 -0.7928 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8205 -0.5280 -2.1848 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2843 -0.7314 -2.0253 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9031 -0.5957 -0.8721 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3749 -0.8103 -0.7619 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9888 0.5686 -0.4997 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.1358 0.4250 0.2567 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9951 1.4999 0.1620 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1125 0.7610 1.1409 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2104 -0.2197 0.4160 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1515 -1.4936 1.2237 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8614 0.3468 0.0838 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1078 0.8133 1.2636 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6357 1.0382 1.0455 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0274 -0.1632 0.3535 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2166 -1.3554 1.2149 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9308 -1.1575 -0.1569 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2767 -1.1447 -0.7485 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6852 -1.5662 1.0089 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8601 0.6484 1.6143 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1743 0.9996 -1.1284 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9765 0.6118 0.4271 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0866 2.7741 0.5150 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6694 1.3232 -1.1632 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8048 2.3835 0.2370 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2772 1.0667 1.5288 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5347 1.6352 0.0436 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4317 -1.2031 0.7108 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9703 -0.7938 -0.9521 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2400 -1.8307 0.2586 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1211 -1.5936 2.5137 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8761 0.2500 2.4638 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4760 -0.4785 2.4700 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5853 1.1625 0.1083 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1454 0.8442 -2.0863 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2900 -0.6056 -2.0056 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1154 -1.1612 -2.8246 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4332 -2.0003 -1.2762 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7624 0.8082 -1.4303 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3076 -1.7008 -0.5277 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5704 0.4456 -2.6155 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4088 -1.3485 -2.7956 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8470 -1.0049 -2.9210 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7866 -1.1864 -1.7045 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6316 -1.4804 0.0768 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2598 1.0129 -1.4744 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.8924 0.9616 -0.0904 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3515 2.0226 -0.5740 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5555 2.2660 0.7111 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6999 0.2327 1.9006 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4716 1.4868 1.6599 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1828 -1.7148 1.5941 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8507 -2.3546 0.6104 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4528 -1.4186 2.0739 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0668 1.2485 -0.5752 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2469 0.2108 2.1833 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5016 1.8411 1.5347 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5413 1.9084 0.3588 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1984 1.2965 2.0026 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2757 -1.7127 1.1325 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3997 -2.2316 0.9899 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1447 -1.0306 2.2810 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 2 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 1 0 19 20 1 0 19 21 1 0 21 22 1 0 22 23 1 0 23 24 1 1 23 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 1 28 10 1 0 28 13 1 0 25 14 1 0 23 17 1 0 1 30 1 0 1 31 1 0 1 32 1 0 2 33 1 1 3 34 1 0 3 35 1 0 4 36 1 0 5 37 1 0 5 38 1 0 6 39 1 0 6 40 1 0 7 41 1 0 7 42 1 0 8 43 1 1 9 44 1 0 9 45 1 0 9 46 1 0 10 47 1 6 11 48 1 0 11 49 1 0 12 50 1 0 12 51 1 0 13 52 1 6 14 53 1 1 15 54 1 0 15 55 1 0 16 56 1 0 18 57 1 0 18 58 1 0 19 59 1 6 20 60 1 0 21 61 1 0 21 62 1 0 22 63 1 0 22 64 1 0 24 65 1 0 24 66 1 0 24 67 1 0 25 68 1 6 26 69 1 0 26 70 1 0 27 71 1 0 27 72 1 0 29 73 1 0 29 74 1 0 29 75 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 NPC600858 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	23496
0.1-0.2	22553
0.2-0.3	3432
0.3-0.4	229
0.4-0.5	81
0.5-0.6	26
0.6-0.7	19
0.7-0.8	1
0.8-0.85	0
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	NPC321381
0.86	High Similarity	NPC136188
0.86	High Similarity	NPC28657
0.7925	Intermediate Similarity	NPC155986
0.7843	Intermediate Similarity	NPC162742
0.7843	Intermediate Similarity	NPC304309
0.7843	Intermediate Similarity	NPC470228
0.7692	Intermediate Similarity	NPC22105
0.7692	Intermediate Similarity	NPC34019
0.7692	Intermediate Similarity	NPC107059
0.7547	Intermediate Similarity	NPC474216
0.7407	Intermediate Similarity	NPC230301
0.7407	Intermediate Similarity	NPC198968
0.7407	Intermediate Similarity	NPC285893
0.7407	Intermediate Similarity	NPC134847
0.7273	Intermediate Similarity	NPC241290
0.7273	Intermediate Similarity	NPC164840
0.7273	Intermediate Similarity	NPC484739
0.7273	Intermediate Similarity	NPC209944
0.7018	Intermediate Similarity	NPC59453
0.6964	Remote Similarity	NPC264245
0.6897	Remote Similarity	NPC603646
0.678	Remote Similarity	NPC473943
0.6727	Remote Similarity	NPC600590
0.6724	Remote Similarity	NPC472265
0.6667	Remote Similarity	NPC488870
0.6607	Remote Similarity	NPC154330
0.65	Remote Similarity	NPC155011
0.6491	Remote Similarity	NPC113733
0.6441	Remote Similarity	NPC1272
0.6441	Remote Similarity	NPC470614
0.6429	Remote Similarity	NPC221758
0.6393	Remote Similarity	NPC47761
0.6379	Remote Similarity	NPC51014
0.6167	Remote Similarity	NPC318495
0.6167	Remote Similarity	NPC33913
0.6129	Remote Similarity	NPC474164
0.6	Remote Similarity	NPC328714
0.6	Remote Similarity	NPC87604
0.5968	Remote Similarity	NPC243985
0.5968	Remote Similarity	NPC280710
0.5968	Remote Similarity	NPC240650
0.5818	Remote Similarity	NPC96319
0.5806	Remote Similarity	NPC477522
0.5763	Remote Similarity	NPC109546
0.5763	Remote Similarity	NPC328313
0.5763	Remote Similarity	NPC317458
0.5763	Remote Similarity	NPC47982
0.5738	Remote Similarity	NPC31564
0.5606	Remote Similarity	NPC601043
0.5606	Remote Similarity	NPC605412
0.5397	Remote Similarity	NPC153987
0.5333	Remote Similarity	NPC151519
0.5333	Remote Similarity	NPC244488
0.5323	Remote Similarity	NPC486085
0.5323	Remote Similarity	NPC317927
0.5312	Remote Similarity	NPC124172
0.5246	Remote Similarity	NPC20688
0.5167	Remote Similarity	NPC81306
0.5161	Remote Similarity	NPC76879
0.5139	Remote Similarity	NPC486119
0.5079	Remote Similarity	NPC23852
0.5077	Remote Similarity	NPC474752
0.5077	Remote Similarity	NPC474683
0.5072	Remote Similarity	NPC5985

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC600858 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7593
0.1-0.2	1399
0.2-0.3	119
0.3-0.4	26
0.4-0.5	8
0.5-0.6	2
0.6-0.7	1
0.7-0.8	1
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.86	High Similarity	NPD6942	Phase 4
0.7407	Intermediate Similarity	NPD7339	Approved
0.6429	Remote Similarity	NPD4786	Phase 1
0.5818	Remote Similarity	NPD3701	Pre-clinical
0.5333	Remote Similarity	NPD3667	Phase 4

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