NPASS Compound

Natural Product: NPC603877

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 85 89 0 0 0 0 0 0 0 0999 V2000 -2.4891 0.0390 4.8214 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8307 0.8021 3.7304 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6647 2.0396 3.8458 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3795 0.2001 2.5626 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7492 0.8615 1.4923 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6970 0.5048 1.3629 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1266 0.6564 -0.1146 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5478 0.5109 -0.1609 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3008 1.5473 -0.6873 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6732 2.5654 -1.0965 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7666 1.5114 -0.7867 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4449 0.4723 -0.3723 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8953 0.3648 -0.4383 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7131 1.3502 -0.9466 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0946 1.2178 -0.9956 C 0 0 0 0 0 0 0 0 0 0 0 0 9.6943 0.0741 -0.5275 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8983 -0.9273 -0.0137 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5425 -0.7768 0.0251 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4171 -0.5357 -0.6368 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5318 -1.5162 0.3813 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9870 -0.9593 1.5196 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3257 -1.6201 2.6946 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4918 -1.1126 1.7247 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0380 -1.2358 -1.7902 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3473 -0.3993 -2.9866 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2495 -2.4620 -2.0567 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9255 -2.7411 -1.2258 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7550 -3.6304 -1.9657 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7010 -1.6190 -0.6541 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9347 -1.5744 -1.3928 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1635 -1.7732 -0.7706 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4485 -1.7311 -1.5151 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1218 -1.9927 0.4699 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0527 -0.2845 -0.7615 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4547 0.2216 -2.1566 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5039 0.7626 0.1895 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8588 0.9870 0.2941 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5881 2.0686 -0.1059 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8715 2.9515 -0.6398 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0308 2.2323 0.0444 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5954 3.4032 -0.4358 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9515 3.5899 -0.3063 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7497 2.6507 0.2824 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1779 1.4819 0.7603 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8081 1.2875 0.6325 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8873 0.1688 5.7329 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5310 0.3817 4.9863 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5558 -1.0260 4.5157 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7184 1.9440 1.8418 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3692 1.0607 2.0162 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8329 1.6172 -0.5270 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2743 2.3463 -1.2027 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9058 -0.3807 0.0541 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2910 2.2567 -1.3216 H 0 0 0 0 0 0 0 0 0 0 0 0 9.7065 2.0205 -1.4054 H 0 0 0 0 0 0 0 0 0 0 0 0 10.7638 -0.0205 -0.5688 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3986 -1.8156 0.3472 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9307 -1.5686 0.4300 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6849 -2.0210 2.4772 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3957 -1.0403 3.6269 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9411 -2.5501 2.9006 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7235 -1.8200 2.5751 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9816 -1.5553 0.8476 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9376 -0.1477 2.0415 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0559 -1.5619 -1.4064 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4537 0.6752 -2.7403 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3427 -0.6743 -3.4444 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6368 -0.5649 -3.8444 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9195 -3.3747 -2.0332 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0561 -2.4261 -3.1467 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6027 -3.4018 -0.3784 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1459 -4.3950 -2.1775 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8987 -1.8117 0.4197 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2198 -1.7301 -2.6109 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0676 -0.8584 -1.2935 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9813 -2.6854 -1.3283 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5145 0.5969 -2.0006 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5557 -0.5825 -2.8813 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8892 1.0974 -2.4628 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1601 1.7217 -0.3214 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9792 4.1600 -0.9057 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3709 4.5154 -0.6902 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.8079 2.8536 0.3556 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8297 0.7534 1.2221 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3811 0.3799 1.0076 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 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 7 19 1 0 19 20 1 1 20 21 1 0 21 22 1 0 21 23 1 0 19 24 1 0 24 25 1 0 24 26 1 0 26 27 1 0 27 28 1 0 27 29 1 0 29 30 1 0 30 31 1 0 31 32 1 0 31 33 2 0 29 34 1 0 34 35 1 6 34 36 1 0 36 37 1 0 37 38 1 0 38 39 2 0 38 40 1 0 40 41 2 0 41 42 1 0 42 43 2 0 43 44 1 0 44 45 2 0 36 5 1 0 45 40 1 0 21 6 1 0 18 13 1 0 34 19 1 0 1 46 1 0 1 47 1 0 1 48 1 0 5 49 1 1 6 50 1 1 7 51 1 6 11 52 1 0 12 53 1 0 14 54 1 0 15 55 1 0 16 56 1 0 17 57 1 0 18 58 1 0 22 59 1 0 22 60 1 0 22 61 1 0 23 62 1 0 23 63 1 0 23 64 1 0 24 65 1 1 25 66 1 0 25 67 1 0 25 68 1 0 26 69 1 0 26 70 1 0 27 71 1 1 28 72 1 0 29 73 1 1 32 74 1 0 32 75 1 0 32 76 1 0 35 77 1 0 35 78 1 0 35 79 1 0 36 80 1 6 41 81 1 0 42 82 1 0 43 83 1 0 44 84 1 0 45 85 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 NPC603877 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	9065
0.1-0.2	36841
0.2-0.3	3215
0.3-0.4	569
0.4-0.5	108
0.5-0.6	49
0.6-0.7	6
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	Natural Product ID
0.7368	Intermediate Similarity	NPC609221
0.7143	Intermediate Similarity	NPC481050
0.6386	Remote Similarity	NPC125106
0.6386	Remote Similarity	NPC472573
0.6341	Remote Similarity	NPC470159
0.6265	Remote Similarity	NPC605086
0.6026	Remote Similarity	NPC200471
0.6026	Remote Similarity	NPC472575
0.5921	Remote Similarity	NPC66761
0.5921	Remote Similarity	NPC483843
0.5921	Remote Similarity	NPC476094
0.5882	Remote Similarity	NPC70403
0.5882	Remote Similarity	NPC177940
0.5844	Remote Similarity	NPC607964
0.5833	Remote Similarity	NPC29704
0.5833	Remote Similarity	NPC470157
0.5769	Remote Similarity	NPC483862
0.5765	Remote Similarity	NPC472571
0.5732	Remote Similarity	NPC252314
0.5714	Remote Similarity	NPC481047
0.5714	Remote Similarity	NPC481045
0.5663	Remote Similarity	NPC210591
0.5632	Remote Similarity	NPC483865
0.5595	Remote Similarity	NPC607428
0.557	Remote Similarity	NPC241951
0.557	Remote Similarity	NPC90614
0.5513	Remote Similarity	NPC475429
0.5513	Remote Similarity	NPC211137
0.5488	Remote Similarity	NPC473088
0.5412	Remote Similarity	NPC473085
0.5412	Remote Similarity	NPC473112
0.5393	Remote Similarity	NPC488916
0.5357	Remote Similarity	NPC609924
0.5281	Remote Similarity	NPC483861
0.5263	Remote Similarity	NPC488902
0.5263	Remote Similarity	NPC488903
0.5244	Remote Similarity	NPC163719
0.5244	Remote Similarity	NPC95810
0.5222	Remote Similarity	NPC483859
0.5222	Remote Similarity	NPC184817
0.5181	Remote Similarity	NPC473871
0.5169	Remote Similarity	NPC483866
0.5122	Remote Similarity	NPC483886
0.5119	Remote Similarity	NPC473758
0.5114	Remote Similarity	NPC483887
0.5114	Remote Similarity	NPC158020
0.5114	Remote Similarity	NPC481486
0.5111	Remote Similarity	NPC174982
0.5111	Remote Similarity	NPC483860
0.506	Remote Similarity	NPC90257
0.506	Remote Similarity	NPC69357
0.5056	Remote Similarity	NPC212768
0.5056	Remote Similarity	NPC475122
0.5056	Remote Similarity	NPC4421
0.5056	Remote Similarity	NPC483878
0.5055	Remote Similarity	NPC188865
0.5055	Remote Similarity	NPC171525

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC603877 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3700
0.1-0.2	5317
0.2-0.3	133
0.3-0.4	0
0.4-0.5	0
0.5-0.6	0
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
		NPD

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