NPASS Compound

Natural Product: NPC592223

Natural Product ID	NPC592223
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(25R)-3beta-{O-beta-D-glucopyranosyloxy}-22alphaN-spirosol-5-ene
IUPAC Name	(2~{R},3~{S},4~{S},5~{R})-2-(hydroxymethyl)-6-(5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-piperidine]-16-yl)oxy-tetrahydropyran-3,4,5-triol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 94100 0 0 0 0 0 0 0 0999 V2000 -9.4168 0.1345 0.6010 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5620 -0.8376 1.3574 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4953 -0.1649 2.1812 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4857 0.5828 1.3457 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9695 -0.3486 0.2976 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0125 -1.0257 -0.4342 N 0 0 0 0 0 0 0 0 0 0 0 0 -7.8673 -1.8113 0.4274 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0068 -1.2446 0.7788 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8194 -0.5466 0.9202 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6178 -1.2836 0.4280 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0757 -0.4998 -0.7473 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6032 -0.6383 -0.8506 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1033 -0.5233 -2.2832 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3097 -1.0180 -2.2263 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0611 -0.7124 -1.1956 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4638 -1.2052 -1.1440 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3276 0.0213 -1.2076 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3431 0.0872 -0.3203 O 0 0 0 0 0 0 0 0 0 0 0 0 6.6193 0.0971 -0.7957 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2464 -1.0729 -0.3691 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7291 -1.0392 0.9005 C 0 0 2 0 0 0 0 0 0 0 0 0 7.3568 -2.2921 1.7084 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8489 -3.4356 1.1302 O 0 0 0 0 0 0 0 0 0 0 0 0 7.3064 0.1331 1.7308 C 0 0 1 0 0 0 0 0 0 0 0 0 8.0298 0.0625 2.9438 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7258 1.3948 1.0485 C 0 0 2 0 0 0 0 0 0 0 0 0 7.1366 2.5302 1.6063 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4688 1.2621 -0.4143 C 0 0 1 0 0 0 0 0 0 0 0 0 8.7082 1.0867 -1.0787 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5464 1.3150 -1.1702 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4630 1.3626 -0.1188 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6413 0.1117 -0.0343 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1878 -0.6487 1.1945 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1829 0.2830 0.0651 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3189 1.6956 -0.0001 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8012 1.8136 0.2292 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6202 0.8806 -0.6442 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7724 1.5819 -1.9892 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9241 0.6679 0.0351 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1269 0.4025 -0.7579 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0449 -0.5448 -1.8973 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.9916 -0.4463 -0.1476 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.8414 0.9593 0.1355 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.1073 0.6162 1.3297 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.2020 -1.4081 2.0340 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9129 0.4537 3.0088 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9231 -0.9978 2.6827 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9768 1.4341 0.8352 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6589 0.8927 1.9983 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5944 -0.2921 -0.8991 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5806 -2.3592 -0.2266 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2835 -2.5097 1.0353 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7470 -0.2563 2.0048 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8388 -2.3486 0.1398 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8907 -1.3571 1.2638 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4870 -0.9318 -1.7093 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3767 -1.7140 -0.5731 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0977 0.5220 -2.6458 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6737 -1.2253 -2.8877 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6854 -1.6345 -3.0642 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5633 -1.7565 -0.1878 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5958 -1.8993 -1.9944 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7909 -0.0051 -2.2416 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6489 0.0426 -1.9247 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8557 -1.0415 0.8715 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2696 -2.2770 1.8591 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8156 -2.1279 2.7285 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7867 -3.2697 0.8608 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2432 0.1051 2.0211 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9397 0.4217 2.8404 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8303 1.5127 1.2402 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2629 3.2904 0.9776 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0856 2.2332 -0.7894 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5167 0.8800 -2.0283 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1684 1.6009 -2.1750 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2707 2.1407 -0.9058 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9654 1.6001 0.8425 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8570 2.2638 -0.3630 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9449 -1.7209 1.1343 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2386 -0.4215 1.3659 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6057 -0.2293 2.0614 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1159 -0.0703 1.1025 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1660 2.3395 0.7623 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1063 2.1782 -0.9759 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1649 2.8545 0.1223 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9843 1.5431 1.2905 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8199 1.9755 -2.1208 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1382 2.5169 -2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4378 0.9664 -2.8324 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1344 1.5357 0.6955 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6786 1.3039 -1.0990 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5081 -0.2219 -2.7825 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1151 -0.6827 -2.2536 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7788 -1.5918 -1.5629 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 4 5 1 0 5 6 1 0 6 7 1 0 5 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 21 24 1 0 24 25 1 0 24 26 1 0 26 27 1 0 26 28 1 0 28 29 1 0 17 30 1 0 30 31 1 0 31 32 1 0 32 33 1 0 32 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 37 38 1 0 37 39 1 0 39 40 1 0 40 41 1 0 7 2 1 0 39 9 1 0 40 5 1 0 37 11 1 0 34 12 1 0 32 15 1 0 28 19 1 0 1 42 1 0 1 43 1 0 1 44 1 0 2 45 1 0 3 46 1 0 3 47 1 0 4 48 1 0 4 49 1 0 6 50 1 0 7 51 1 0 7 52 1 0 9 53 1 0 10 54 1 0 10 55 1 0 11 56 1 0 12 57 1 0 13 58 1 0 13 59 1 0 14 60 1 0 16 61 1 0 16 62 1 0 17 63 1 0 19 64 1 0 21 65 1 6 22 66 1 0 22 67 1 0 23 68 1 0 24 69 1 1 25 70 1 0 26 71 1 6 27 72 1 0 28 73 1 6 29 74 1 0 30 75 1 0 30 76 1 0 31 77 1 0 31 78 1 0 33 79 1 0 33 80 1 0 33 81 1 0 34 82 1 0 35 83 1 0 35 84 1 0 36 85 1 0 36 86 1 0 38 87 1 0 38 88 1 0 38 89 1 0 39 90 1 0 40 91 1 0 41 92 1 0 41 93 1 0 41 94 1 0 M END

Standard InCHIKey	XMLLJGHZPHTUKK-ZOYZCTNRSA-N
Standard InCHI	InChI=1S/C33H53NO7/c1-17-7-12-33(34-15-17)18(2)26-24(41-33)14-23-21-6-5-19-13-20(8-10-31(19,3)22(21)9-11-32(23,26)4)39-30-29(38)28(37)27(36)25(16-35)40-30/h5,17-18,20-30,34-38H,6-16H2,1-4H3/t17?,18?,20?,21?,22?,23?,24?,25-,26?,27-,28+,29-,30?,31?,32?,33?/m1/s1
SMILES	CC1CCC2(NC1)OC1CC3C4CC=C5CC(OC6O[C@H](CO)[C@@H](O)[C@H](O)[C@H]6O)CCC5(C)C4CCC3(C)C1C2C

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
NPO24724	Solanum aculeastrum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24724	Solanum aculeastrum	Species	Solanaceae	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 NPC592223 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	22286
0.1-0.2	23442
0.2-0.3	3377
0.3-0.4	610
0.4-0.5	89
0.5-0.6	36
0.6-0.7	10
0.7-0.8	1
0.8-0.85	4
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8353	Intermediate Similarity	NPC15249
0.8353	Intermediate Similarity	NPC25455
0.8022	Intermediate Similarity	NPC150057
0.8022	Intermediate Similarity	NPC147753
0.7609	Intermediate Similarity	NPC122819
0.7	Intermediate Similarity	NPC485606
0.6796	Remote Similarity	NPC287885
0.675	Remote Similarity	NPC147835
0.675	Remote Similarity	NPC253645
0.675	Remote Similarity	NPC85001
0.675	Remote Similarity	NPC95920
0.6477	Remote Similarity	NPC296686
0.6333	Remote Similarity	NPC181845
0.6	Remote Similarity	NPC22140
0.6	Remote Similarity	NPC243728
0.6	Remote Similarity	NPC158088
0.5862	Remote Similarity	NPC282669
0.5816	Remote Similarity	NPC295980
0.5673	Remote Similarity	NPC6806
0.5577	Remote Similarity	NPC477809
0.5534	Remote Similarity	NPC98696
0.549	Remote Similarity	NPC14704
0.5446	Remote Similarity	NPC470432
0.5446	Remote Similarity	NPC230507
0.5446	Remote Similarity	NPC94272
0.534	Remote Similarity	NPC305423
0.534	Remote Similarity	NPC113044
0.534	Remote Similarity	NPC283829
0.534	Remote Similarity	NPC161676
0.5321	Remote Similarity	NPC475550
0.5278	Remote Similarity	NPC73243
0.5278	Remote Similarity	NPC244086
0.5278	Remote Similarity	NPC84956
0.5278	Remote Similarity	NPC102016
0.5278	Remote Similarity	NPC95051
0.5234	Remote Similarity	NPC300557
0.5185	Remote Similarity	NPC480555
0.5185	Remote Similarity	NPC150372
0.5182	Remote Similarity	NPC247037
0.5149	Remote Similarity	NPC297058
0.5104	Remote Similarity	NPC486114
0.5102	Remote Similarity	NPC272015
0.5088	Remote Similarity	NPC477811
0.5059	Remote Similarity	NPC155985
0.5059	Remote Similarity	NPC601115
0.5057	Remote Similarity	NPC207617
0.5057	Remote Similarity	NPC607440
0.5056	Remote Similarity	NPC473890
0.5047	Remote Similarity	NPC602423
0.5044	Remote Similarity	NPC218571
0.5044	Remote Similarity	NPC487615
0.5044	Remote Similarity	NPC249265

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC592223 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7231
0.1-0.2	1796
0.2-0.3	108
0.3-0.4	12
0.4-0.5	1
0.5-0.6	0
0.6-0.7	0
0.7-0.8	1
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8022	Intermediate Similarity	NPD8450	Suspended
0.7609	Intermediate Similarity	NPD8449	Approved

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