NPASS Compound

Natural Product: NPC65590

Natural Product ID	NPC65590
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Rubuside A
IUPAC Name	[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] (2R,4aS,6aR,6aS,6bR,8aR,10R,11R,12aR)-10,11-dihydroxy-1,2,6a,6b,9,9,12a-heptamethyl-3,4,5,6,6a,7,8,8a,10,11,12,13-dodecahydro-2H-picene-4a-carboxylate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1077613
PubChem CID	44557350
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

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 101106 0 0 0 0 0 0 0 0999 V2000 2.6469 -1.1832 4.5255 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8285 -0.7035 3.0628 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3995 0.6601 3.1309 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6066 1.7667 2.5446 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0273 1.3526 1.2239 C 0 0 2 0 0 0 0 0 0 0 0 0 1.2151 2.4014 0.5591 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2320 2.4508 0.7110 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9964 1.1801 0.7331 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8822 1.1579 1.9678 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0784 -0.0103 0.8263 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3568 -1.1897 0.3414 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6468 -1.5071 -0.3744 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5736 -0.3364 -0.2673 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.8412 -0.5205 -1.0416 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.6954 -0.6892 -2.5098 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4809 -1.7968 -0.5033 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9077 -1.9626 -0.8991 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.7366 -0.7786 -0.5329 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.1440 0.5376 -1.0340 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8919 1.6184 -0.2324 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4715 0.7386 -2.4533 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7202 0.6306 -0.6379 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1309 1.9680 -0.9983 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7093 2.1516 -0.6705 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8600 0.9575 -0.5003 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8653 0.7955 -1.6598 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0484 -0.9424 -0.9310 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4032 -3.0470 -0.1364 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2175 0.1342 1.5178 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5263 -0.8166 2.3507 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6765 -2.0058 2.6891 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1784 1.0480 0.3361 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3195 1.7753 -0.6881 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0983 0.0544 0.5221 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1286 -0.1187 -0.3924 C 0 0 1 0 0 0 0 0 0 0 0 0 6.5012 0.0317 0.2382 C 0 0 1 0 0 0 0 0 0 0 0 0 7.5109 -0.1098 -0.8674 C 0 0 2 0 0 0 0 0 0 0 0 0 6.9172 -0.3181 -2.2185 C 0 0 1 0 0 0 0 0 0 0 0 0 5.7640 -1.2798 -2.2340 C 0 0 1 0 0 0 0 0 0 0 0 0 6.2503 -2.6361 -2.6993 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2006 -3.5305 -2.8732 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0965 -1.3567 -1.0238 O 0 0 0 0 0 0 0 0 0 0 0 0 6.6154 0.8964 -2.8807 O 0 0 0 0 0 0 0 0 0 0 0 0 8.4990 -1.0441 -0.5568 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5753 1.2758 0.8643 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7960 -0.6751 4.9976 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5595 -0.8237 5.0745 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6458 -2.2706 4.5904 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5535 -1.4861 2.6755 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5886 0.9640 4.2156 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4349 0.6926 2.6931 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8181 2.0912 3.2573 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2420 2.6636 2.3858 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4677 2.3994 -0.5216 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6527 3.3877 0.9149 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4796 3.0766 1.6155 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6687 3.0642 -0.1376 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8557 0.1836 2.4935 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9046 1.5327 1.7682 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4569 1.8901 2.7173 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3271 -1.9993 0.3932 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0891 -2.3520 0.1945 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4633 -1.8635 -1.3879 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8998 -0.3105 0.8188 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9671 -1.4887 -2.7106 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4028 0.2003 -3.0699 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6745 -1.1167 -2.8827 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4077 -1.8515 0.5988 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8802 -2.6345 -0.9452 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0663 -2.2698 -1.9524 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7340 -0.6908 0.5857 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3926 1.8045 0.7423 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8777 2.5221 -0.8502 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9525 1.3049 -0.0999 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8972 -0.2177 -2.8796 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3130 1.4780 -2.6080 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6798 1.0448 -3.1242 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7111 0.6082 0.4969 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3257 2.1496 -2.0809 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7912 2.7237 -0.4791 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2441 2.7841 -1.4881 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6579 2.8483 0.2217 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1344 -0.0015 -2.3485 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7998 1.7710 -2.1801 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1580 0.5668 -1.2969 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4353 -1.6554 -0.3430 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2358 -2.8772 0.8290 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0688 -2.9633 2.3662 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4051 -1.8355 2.6214 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7591 -2.1225 3.8266 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0377 0.6409 -1.1928 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6159 -0.7893 0.9888 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0651 0.8749 -0.9177 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7250 -0.7615 -2.8597 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0358 -0.9231 -2.9927 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9714 -3.0030 -1.9143 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8596 -2.4925 -3.6148 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0507 -3.6151 -3.8482 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1778 1.6291 -2.5423 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5885 -1.0295 0.4441 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4779 1.5227 1.1252 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 7 8 1 0 8 9 1 1 8 10 1 0 10 11 2 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 6 14 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 19 21 1 0 19 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 6 18 27 1 0 17 28 1 0 10 29 1 0 29 30 2 0 30 31 1 0 5 32 1 6 32 33 2 0 32 34 1 0 34 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 1 0 39 42 1 0 38 43 1 0 37 44 1 0 36 45 1 0 30 2 1 0 42 35 1 0 29 5 1 0 25 8 1 0 25 13 1 0 22 14 1 0 1 46 1 0 1 47 1 0 1 48 1 0 2 49 1 6 3 50 1 0 3 51 1 0 4 52 1 0 4 53 1 0 6 54 1 0 6 55 1 0 7 56 1 0 7 57 1 0 9 58 1 0 9 59 1 0 9 60 1 0 11 61 1 0 12 62 1 0 12 63 1 0 13 64 1 1 15 65 1 0 15 66 1 0 15 67 1 0 16 68 1 0 16 69 1 0 17 70 1 6 18 71 1 1 20 72 1 0 20 73 1 0 20 74 1 0 21 75 1 0 21 76 1 0 21 77 1 0 22 78 1 1 23 79 1 0 23 80 1 0 24 81 1 0 24 82 1 0 26 83 1 0 26 84 1 0 26 85 1 0 27 86 1 0 28 87 1 0 31 88 1 0 31 89 1 0 31 90 1 0 35 91 1 6 36 92 1 1 37 93 1 6 38 94 1 6 39 95 1 6 40 96 1 0 40 97 1 0 41 98 1 0 43 99 1 0 44100 1 0 45101 1 0 M END

Standard InCHIKey	OFWIRPXDLBDEFC-NRAYHWQBSA-N
Standard InCHI	InChI=1S/C36H56O9/c1-18-10-13-36(31(43)45-30-28(41)27(40)26(39)22(17-37)44-30)15-14-34(6)20(25(36)19(18)2)8-9-24-33(5)16-21(38)29(42)32(3,4)23(33)11-12-35(24,34)7/h8,18,21-24,26-30,37-42H,9-17H2,1-7H3/t18-,21-,22-,23+,24-,26-,27+,28-,29+,30+,33+,34-,35-,36+/m1/s1
SMILES	C[C@@H]1CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)C[C@H]([C@@H](C(C)(C)[C@@H]5CC[C@@]34C)O)O)C2=C1C)C(=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)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
NPO23655.1	Rubus ellipticus	Under-species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[19795885]
NPO23655.1	Rubus ellipticus	Under-species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[38455614]
NPO23655.1	Rubus ellipticus	Under-species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]

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

Activity Type	# Activity
IC50	1

Activity Type	# Activity
Others	1

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
NPT2	Others	Unspecified	n.a.	IC50	=	2540000.0	nM	PMID[21142180]

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 NPC65590 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	19054
0.1-0.2	25351
0.2-0.3	4549
0.3-0.4	783
0.4-0.5	97
0.5-0.6	12
0.6-0.7	6
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC125923
0.8816	High Similarity	NPC212968
0.7875	Intermediate Similarity	NPC64106
0.7625	Intermediate Similarity	NPC190837
0.7011	Intermediate Similarity	NPC161434
0.7011	Intermediate Similarity	NPC195132
0.6824	Remote Similarity	NPC7870
0.6824	Remote Similarity	NPC75747
0.6667	Remote Similarity	NPC605954
0.6437	Remote Similarity	NPC310014
0.6437	Remote Similarity	NPC269315
0.6	Remote Similarity	NPC102914
0.5843	Remote Similarity	NPC116794
0.5761	Remote Similarity	NPC220984
0.573	Remote Similarity	NPC285576
0.5714	Remote Similarity	NPC68419
0.5652	Remote Similarity	NPC271138
0.5652	Remote Similarity	NPC110139
0.5652	Remote Similarity	NPC108709
0.5393	Remote Similarity	NPC191763
0.5275	Remote Similarity	NPC167383
0.5217	Remote Similarity	NPC46388
0.5213	Remote Similarity	NPC604133
0.5053	Remote Similarity	NPC48249

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC65590 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7059
0.1-0.2	2010
0.2-0.3	77
0.3-0.4	4
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