NPASS Compound

Natural Product: NPC606582

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 121127 0 0 0 0 0 0 0 0999 V2000 -8.0145 4.2786 -1.6989 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1655 3.0709 -2.0191 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.5365 3.3313 -3.3642 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7381 2.5773 -4.3469 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7078 4.4267 -3.5519 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.0337 1.8644 -2.1434 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8549 0.9923 -0.9330 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4474 0.3954 -0.8943 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.3736 -0.6235 -2.0138 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3391 -0.3436 0.3943 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9136 -0.7743 0.6653 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9824 0.3777 0.7484 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1178 1.0572 2.0843 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2364 1.3965 -0.3317 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2355 2.2686 -0.5600 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9784 2.2100 0.2113 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2827 3.2611 0.1459 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6803 0.9979 0.9388 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2061 0.6245 1.0688 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3335 0.6147 -0.3262 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4650 1.7134 1.8484 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6758 1.3758 2.5801 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2612 -0.0132 2.3704 C 0 0 2 0 0 0 0 0 0 0 0 0 3.2450 0.0106 1.3933 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5218 -0.0813 1.8231 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1607 1.1970 1.8454 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3694 1.1077 2.4566 C 0 0 2 0 0 0 0 0 0 0 0 0 7.4904 1.6264 1.6095 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6643 1.5672 2.0862 O 0 0 0 0 0 0 0 0 0 0 0 0 7.2183 2.1403 0.3678 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7706 -0.1894 3.0484 C 0 0 1 0 0 0 0 0 0 0 0 0 6.3209 -0.3459 4.3771 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4939 -1.4101 2.2197 C 0 0 2 0 0 0 0 0 0 0 0 0 7.6192 -1.9928 1.6932 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4814 -0.9766 1.1607 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0124 -1.9924 0.3820 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4446 -1.9209 -0.9492 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3616 -1.6273 -1.7971 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8483 -1.3314 -3.0646 C 0 0 2 0 0 0 0 0 0 0 0 0 3.9093 -0.4651 -3.8202 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1422 -0.0844 -4.9952 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7006 -0.0232 -3.2524 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1778 -2.6204 -3.7631 C 0 0 1 0 0 0 0 0 0 0 0 0 6.2680 -2.5720 -4.5921 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3761 -3.7045 -2.7213 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1657 -4.2704 -2.3442 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0727 -3.1642 -1.4635 C 0 0 1 0 0 0 0 0 0 0 0 0 7.4493 -3.0551 -1.6909 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2544 -1.0659 2.2668 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1338 -1.7579 3.6453 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7529 -2.1830 1.3820 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0195 -1.7906 0.1027 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1278 -0.6241 1.8479 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8772 -1.7761 1.1798 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3545 -1.3947 1.1850 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5672 -0.0943 0.4605 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5117 -0.3849 -1.0097 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4586 1.4837 -1.1285 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0899 2.8608 -0.9716 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6981 5.1680 -2.2979 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.0828 4.1198 -1.9578 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9226 4.5884 -0.6384 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0136 4.4740 -4.3174 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7522 1.2530 -3.0282 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.1240 2.1527 -2.1802 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0468 1.6136 -0.0337 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.6394 0.2039 -0.9557 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3929 -0.8207 -2.3784 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6856 -0.2869 -2.8334 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9643 -1.5835 -1.6416 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7026 0.1940 1.2776 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9349 -1.2860 0.2912 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9251 -1.2661 1.6827 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6710 -1.5489 -0.0577 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7857 2.1311 2.0387 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6794 0.4862 2.9091 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2119 1.1270 2.3042 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3733 3.0132 -1.3270 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9890 1.1928 2.0169 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0660 -0.2302 -0.9489 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1394 1.5086 -0.8412 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4062 0.8184 -0.4299 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3228 2.0917 2.5786 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6670 2.6185 1.2244 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5077 1.5707 3.6846 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4909 2.1310 2.3485 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8761 -0.1489 3.3242 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4860 -0.3017 2.9372 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3365 1.8451 3.3216 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0023 2.4245 -0.2261 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8965 -0.1591 3.1656 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3912 -1.3165 4.5806 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0041 -2.1664 2.8947 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9654 -1.4189 0.9728 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1085 -0.3349 0.4469 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1212 -1.0521 -1.0557 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7793 -0.7360 -2.9324 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2268 0.8118 -3.6142 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2762 -2.8865 -4.3844 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9849 -1.9619 -4.3537 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0137 -4.5087 -3.1276 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3902 -3.7375 -2.5826 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9517 -3.9775 -0.6979 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8077 -3.8139 -2.1779 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1406 -2.0025 4.0308 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5152 -2.6764 3.5502 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6103 -1.1112 4.3663 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7457 -2.5194 1.8196 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1309 -3.1070 1.4482 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0376 -2.5443 -0.5432 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6963 -0.4523 2.7874 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8200 -2.7040 1.7689 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4953 -1.9967 0.1798 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6882 -1.3777 2.2411 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8918 -2.1997 0.6622 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1016 0.4119 -1.6391 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0151 -1.3823 -1.2063 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5474 -0.5566 -1.4379 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1507 1.4112 -2.2131 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2973 3.6085 -1.1622 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5243 3.0292 0.0123 H 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 2 3 1 0 3 4 2 0 3 5 1 0 2 6 1 0 6 7 1 0 7 8 1 0 8 9 1 6 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 1 12 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 16 18 1 0 18 19 1 0 19 20 1 6 19 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 2 0 28 30 1 0 27 31 1 0 31 32 1 0 31 33 1 0 33 34 1 0 33 35 1 0 35 36 1 0 36 37 1 0 37 38 1 0 38 39 1 0 39 40 1 0 40 41 2 0 40 42 1 0 39 43 1 0 43 44 1 0 43 45 1 0 45 46 1 0 45 47 1 0 47 48 1 0 23 49 1 0 49 50 1 1 49 51 1 0 51 52 1 0 49 53 1 0 53 54 1 0 54 55 1 0 55 56 1 0 56 57 1 6 14 58 1 0 58 59 1 0 59 2 1 0 58 8 1 0 56 12 1 0 56 18 1 0 53 19 1 0 35 25 1 0 47 37 1 0 1 60 1 0 1 61 1 0 1 62 1 0 5 63 1 0 6 64 1 0 6 65 1 0 7 66 1 0 7 67 1 0 9 68 1 0 9 69 1 0 9 70 1 0 10 71 1 0 10 72 1 0 11 73 1 0 11 74 1 0 13 75 1 0 13 76 1 0 13 77 1 0 15 78 1 0 18 79 1 1 20 80 1 0 20 81 1 0 20 82 1 0 21 83 1 0 21 84 1 0 22 85 1 0 22 86 1 0 23 87 1 1 25 88 1 1 27 89 1 1 30 90 1 0 31 91 1 1 32 92 1 0 33 93 1 1 34 94 1 0 35 95 1 6 37 96 1 1 39 97 1 1 42 98 1 0 43 99 1 6 44100 1 0 45101 1 6 46102 1 0 47103 1 1 48104 1 0 50105 1 0 50106 1 0 50107 1 0 51108 1 0 51109 1 0 52110 1 0 53111 1 1 54112 1 0 54113 1 0 55114 1 0 55115 1 0 57116 1 0 57117 1 0 57118 1 0 58119 1 6 59120 1 0 59121 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 NPC606582 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	20105
0.1-0.2	25762
0.2-0.3	3398
0.3-0.4	453
0.4-0.5	85
0.5-0.6	15
0.6-0.7	17
0.7-0.8	0
0.8-0.85	3
0.85-0.9	0
0.9-0.95	4
0.95-1	4

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC482741
1.0	High Similarity	NPC482745
1.0	High Similarity	NPC482743
1.0	High Similarity	NPC146753
0.9	High Similarity	NPC482747
0.9	High Similarity	NPC202666
0.9	High Similarity	NPC471961
0.9	High Similarity	NPC242015
0.8061	Intermediate Similarity	NPC482755
0.8021	Intermediate Similarity	NPC471965
0.8021	Intermediate Similarity	NPC482749
0.7979	Intermediate Similarity	NPC482748
0.7912	Intermediate Similarity	NPC482752
0.77	Intermediate Similarity	NPC262199
0.7576	Intermediate Similarity	NPC14617
0.732	Intermediate Similarity	NPC482750
0.7273	Intermediate Similarity	NPC482746
0.7255	Intermediate Similarity	NPC482734
0.7255	Intermediate Similarity	NPC182342
0.7255	Intermediate Similarity	NPC482727
0.7255	Intermediate Similarity	NPC471964
0.7143	Intermediate Similarity	NPC309780
0.71	Intermediate Similarity	NPC482717
0.6792	Remote Similarity	NPC247315
0.6792	Remote Similarity	NPC482728
0.6667	Remote Similarity	NPC482751
0.6635	Remote Similarity	NPC285091
0.6598	Remote Similarity	NPC471967
0.6574	Remote Similarity	NPC482737
0.6509	Remote Similarity	NPC482722
0.6509	Remote Similarity	NPC471963
0.6509	Remote Similarity	NPC482729
0.6509	Remote Similarity	NPC482742
0.6509	Remote Similarity	NPC482744
0.6486	Remote Similarity	NPC471962
0.6436	Remote Similarity	NPC482726
0.6422	Remote Similarity	NPC482735
0.6121	Remote Similarity	NPC482736
0.6121	Remote Similarity	NPC482738
0.6034	Remote Similarity	NPC482739
0.5934	Remote Similarity	NPC4036
0.5934	Remote Similarity	NPC65120
0.5934	Remote Similarity	NPC145067
0.5934	Remote Similarity	NPC233455
0.5934	Remote Similarity	NPC158030
0.5752	Remote Similarity	NPC482740
0.5638	Remote Similarity	NPC482712
0.5638	Remote Similarity	NPC74751
0.5505	Remote Similarity	NPC275343
0.5269	Remote Similarity	NPC96095
0.5143	Remote Similarity	NPC224121
0.5126	Remote Similarity	NPC120116
0.5086	Remote Similarity	NPC118440
0.5044	Remote Similarity	NPC472949
0.5043	Remote Similarity	NPC131469

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC606582 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6302
0.1-0.2	2795
0.2-0.3	45
0.3-0.4	2
0.4-0.5	2
0.5-0.6	3
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9	High Similarity	NPD8328	Phase 2
0.5934	Remote Similarity	NPD7515	Phase 2
0.5638	Remote Similarity	NPD7748	Pre-clinical
0.5354	Remote Similarity	NPD7902	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