NPASS Compound

Natural Product: NPC39631

Natural Product ID	NPC39631
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	OGAJKHIMOFQOPT-LPRGFTSCSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	21595563
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0000676] Taxanes and derivatives

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 -0.4848 -2.6074 2.7141 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4463 -1.8282 1.8315 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1675 -1.3971 0.5954 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1876 -1.7135 0.0681 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7047 -0.8087 -0.9758 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7578 0.6585 -0.6145 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9603 1.3710 -1.9159 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9165 0.8790 0.2674 C 0 0 2 0 0 0 0 0 0 0 0 0 2.0838 2.3600 0.4942 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8606 3.0521 0.8878 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4574 2.4670 0.6260 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6129 3.6332 -0.2670 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6236 4.1653 0.0403 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5236 1.0897 0.1071 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7886 0.6466 -0.5738 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3231 -0.6602 0.0063 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.1693 -0.4763 1.2175 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8134 -1.4490 2.2678 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6772 -0.9243 3.5428 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1026 -1.4711 -0.9812 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6819 -2.7589 -0.3821 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4720 -1.8479 -2.2634 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2844 -0.7655 -1.3669 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6935 1.5626 -0.9519 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1575 2.0830 -2.0907 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6225 1.6080 -3.0890 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2097 3.1240 -2.1061 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2656 2.6414 1.8004 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9396 2.1266 3.0279 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1265 1.4770 3.0842 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7418 2.2816 4.2627 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1431 0.4701 -0.2960 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9507 -0.4486 0.3782 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5186 -0.8784 1.5013 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2045 -0.9200 -0.1129 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6912 -0.4740 -1.3175 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9126 -0.9377 -1.7891 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6392 -1.8440 -1.0537 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1617 -2.3039 0.1641 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9440 -1.8236 0.6054 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0048 -1.2842 -1.2896 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2846 -3.0237 -0.4070 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3606 -1.9911 3.0312 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0600 -3.4712 2.1292 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0257 -3.0442 3.5513 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9582 -1.6795 0.9018 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1894 -0.9209 -1.9793 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0580 1.2741 -2.5921 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7430 0.7693 -2.4741 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3502 2.3750 -1.8837 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7780 0.3249 1.2161 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8899 2.4219 1.2988 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6009 2.7789 -0.3926 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0053 3.5357 1.9083 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6826 3.4931 -1.3422 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4441 4.3447 0.0264 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4733 0.4379 1.0431 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4076 0.3044 -1.5595 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2738 0.5727 1.5549 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2276 -0.7251 0.9747 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4639 -2.3573 2.3291 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4186 -0.3265 3.7298 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9525 -3.2856 0.2283 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0705 -3.3833 -1.2276 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5726 -2.5337 0.2254 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7755 -2.7351 -2.1822 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0688 -1.0565 -2.8914 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3183 -2.2887 -2.8816 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7919 -1.4366 -1.9058 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1592 2.6358 -1.7986 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3454 3.4577 -3.1723 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9638 3.9860 -1.4751 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8222 1.3469 4.8414 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3222 3.0586 4.9340 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7526 2.6016 3.9820 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1610 0.2362 -1.9326 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3200 -0.6027 -2.7356 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5859 -2.2308 -1.3755 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6935 -3.0151 0.7796 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5767 -2.1891 1.5608 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9991 -2.2319 -1.4886 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0818 -3.5013 -0.1214 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 6 6 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 11 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 16 20 1 6 20 21 1 0 20 22 1 0 20 23 1 0 15 24 1 0 24 25 1 0 25 26 2 0 25 27 1 0 11 28 1 1 28 29 1 0 29 30 2 0 29 31 1 0 8 32 1 0 32 33 1 0 33 34 2 0 33 35 1 0 35 36 2 0 36 37 1 0 37 38 2 0 38 39 1 0 39 40 2 0 5 41 1 0 4 42 1 0 18 2 1 0 40 35 1 0 16 3 1 0 14 6 1 0 13 10 1 0 1 43 1 0 1 44 1 0 1 45 1 0 4 46 1 1 5 47 1 6 7 48 1 0 7 49 1 0 7 50 1 0 8 51 1 1 9 52 1 0 9 53 1 0 10 54 1 1 12 55 1 0 12 56 1 0 14 57 1 1 15 58 1 6 17 59 1 0 17 60 1 0 18 61 1 1 19 62 1 0 21 63 1 0 21 64 1 0 21 65 1 0 22 66 1 0 22 67 1 0 22 68 1 0 23 69 1 0 27 70 1 0 27 71 1 0 27 72 1 0 31 73 1 0 31 74 1 0 31 75 1 0 36 76 1 0 37 77 1 0 38 78 1 0 39 79 1 0 40 80 1 0 41 81 1 0 42 82 1 0 M END

Standard InCHIKey	OGAJKHIMOFQOPT-LPRGFTSCSA-N
Standard InCHI	InChI=1S/C31H40O11/c1-15-19(34)13-30(28(4,5)38)22(15)23(35)25(36)29(6)20(41-27(37)18-10-8-7-9-11-18)12-21-31(14-39-21,42-17(3)33)24(29)26(30)40-16(2)32/h7-11,19-21,23-26,34-36,38H,12-14H2,1-6H3/t19-,20-,21+,23+,24-,25-,26-,29+,30-,31-/m0/s1
SMILES	CC1=C2[C@H]([C@@H]([C@]3(C)[C@H](C[C@@H]4[C@@](CO4)([C@H]3[C@@H]([C@@]2(C[C@@H]1O)C(C)(C)O)OC(=O)C)OC(=O)C)OC(=O)c1ccccc1)O)O

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
NPO11132	Alangium longiflorum	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30106296]
NPO11819	Trichophyton megnini	Species	Arthrodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11132	Alangium longiflorum	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7785	Boletus fomentarius	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12272	Calceolaria petiolaris	Species	Calceolariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3362	Dictyostelium mucoroides	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10084	Equisetum hyemale	Species	Equisetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO563	Leucopaxillus cerealis	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21703	Maianthemum atropurpureum	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27451	Ophiocordyceps sinensis	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10953	Papaver strigosum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11936	Ptilocaulis walpersi	Species	Axinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22296	Rheum tataricum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10487	Rosa americana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15125.1	Taxus wallichiana var. chinensis	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15125.1	Taxus wallichiana var. chinensis	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10084	Equisetum hyemale	Species	Equisetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27451	Ophiocordyceps sinensis	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27451	Ophiocordyceps sinensis	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10084	Equisetum hyemale	Species	Equisetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22296	Rheum tataricum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27451	Ophiocordyceps sinensis	Species	Ophiocordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10953	Papaver strigosum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10487	Rosa americana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11132	Alangium longiflorum	Species	Cornaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO563	Leucopaxillus cerealis	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3362	Dictyostelium mucoroides	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11936	Ptilocaulis walpersi	Species	Axinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12615	Athrotaxis selaginoides	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21703	Maianthemum atropurpureum	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12272	Calceolaria petiolaris	Species	Calceolariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7785	Boletus fomentarius	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11819	Trichophyton megnini	Species	Arthrodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10084	Equisetum hyemale	Species	Equisetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15125.1	Taxus wallichiana var. chinensis	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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 NPC39631 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	9471
0.1-0.2	36725
0.2-0.3	3025
0.3-0.4	588
0.4-0.5	32
0.5-0.6	12
0.6-0.7	1
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8986	High Similarity	NPC311825
0.7273	Intermediate Similarity	NPC92867
0.7051	Intermediate Similarity	NPC20255
0.7051	Intermediate Similarity	NPC125882
0.6923	Remote Similarity	NPC38696
0.5882	Remote Similarity	NPC240115
0.5882	Remote Similarity	NPC209592
0.5811	Remote Similarity	NPC475877
0.56	Remote Similarity	NPC165578
0.5349	Remote Similarity	NPC132599
0.5319	Remote Similarity	NPC48599
0.5256	Remote Similarity	NPC602903
0.5227	Remote Similarity	NPC476077
0.5169	Remote Similarity	NPC473611
0.5114	Remote Similarity	NPC229545
0.5114	Remote Similarity	NPC134685
0.5114	Remote Similarity	NPC609501

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC39631 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3291
0.1-0.2	5657
0.2-0.3	189
0.3-0.4	12
0.4-0.5	1
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