NPASS Compound

Natural Product: NPC145287

Natural Product ID	NPC145287
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Rehmaglutoside A
IUPAC Name	[(1S,4aR,5R,7S,7aS)-7-hydroxy-7-methyl-1-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-4a,5,6,7a-tetrahydro-1H-cyclopenta[c]pyran-5-yl] (E)-3-phenylprop-2-enoate
Synonyms	Rehmaglutoside A
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2177296
PubChem CID	71453615
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0004081] Iridoid O-glycosides

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 64 67 0 0 0 0 0 0 0 0999 V2000 -5.3300 3.4520 2.5783 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2999 2.5148 2.4715 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6243 1.5133 1.3833 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5792 0.6093 1.3156 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6442 -0.2313 0.2343 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6118 -1.1407 0.2575 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8549 -1.0670 -0.9263 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1597 -2.3069 -1.5837 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4409 -2.6139 -2.7245 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1352 -2.3586 -2.6773 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4898 -1.7838 -1.4730 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4178 -0.9233 -0.6416 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0808 0.4816 -0.7652 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8965 1.5711 -0.5680 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1428 0.6959 0.1315 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7246 0.4518 -2.1417 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5629 -0.8260 -1.9657 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5252 -0.5303 -1.0025 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8827 -0.6363 -1.1570 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3115 -1.0367 -2.2687 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8295 -0.3013 -0.0806 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1233 -0.3989 -0.2198 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1098 -0.0831 0.8056 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7812 0.3630 2.0665 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7285 0.6601 3.0334 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0738 0.5090 2.7412 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4378 0.0632 1.4850 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4645 -0.2216 0.5508 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9299 -1.0591 0.2384 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.1270 -0.1737 0.4869 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.8820 0.7284 1.6879 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.9964 1.5712 1.7887 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2516 -0.9491 0.6306 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0693 -1.6258 -1.0211 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5419 3.7223 1.6386 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3395 2.9915 2.1882 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1288 1.9832 3.4237 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7311 1.9852 0.4074 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6724 0.3931 -0.6986 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2827 -0.2622 -1.5346 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9489 -3.0315 -3.5704 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4575 -2.5785 -3.5337 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9375 -2.6277 -0.9036 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2252 -1.2580 0.4376 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7279 1.6441 -1.2641 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1821 1.5797 0.5068 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3065 2.5403 -0.6772 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9906 0.1475 0.9343 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3609 1.3295 -2.3290 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0032 0.3609 -2.9507 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9702 -1.1746 -2.9267 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4380 0.0403 0.8665 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4805 -0.7452 -1.1846 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7587 0.4949 2.3383 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4763 1.0107 4.0247 H 0 0 0 0 0 0 0 0 0 0 0 0 9.8500 0.7278 3.4620 H 0 0 0 0 0 0 0 0 0 0 0 0 10.4953 -0.0660 1.2251 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7814 -0.5674 -0.4192 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8212 -1.8703 0.9772 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2032 0.5070 -0.3900 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7622 0.1253 2.6155 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2202 1.6702 2.7460 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0131 -1.8429 0.9841 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9116 -2.1462 -1.0853 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 0 9 10 2 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 13 15 1 1 13 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 2 0 19 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 24 25 1 0 25 26 2 0 26 27 1 0 27 28 2 0 5 29 1 0 29 30 1 0 30 31 1 0 31 32 1 0 30 33 1 0 29 34 1 0 31 3 1 0 12 7 1 0 28 23 1 0 17 11 1 0 1 35 1 0 2 36 1 0 2 37 1 0 3 38 1 6 5 39 1 6 7 40 1 6 9 41 1 0 10 42 1 0 11 43 1 1 12 44 1 1 14 45 1 0 14 46 1 0 14 47 1 0 15 48 1 0 16 49 1 0 16 50 1 0 17 51 1 6 21 52 1 0 22 53 1 0 24 54 1 0 25 55 1 0 26 56 1 0 27 57 1 0 28 58 1 0 29 59 1 1 30 60 1 6 31 61 1 1 32 62 1 0 33 63 1 0 34 64 1 0 M END

Standard InCHIKey	UHNGWGBLRLGYHE-LKBMYYCMSA-N
Standard InCHI	InChI=1S/C24H30O10/c1-24(30)11-15(32-17(26)8-7-13-5-3-2-4-6-13)14-9-10-31-22(18(14)24)34-23-21(29)20(28)19(27)16(12-25)33-23/h2-10,14-16,18-23,25,27-30H,11-12H2,1H3/b8-7+/t14-,15+,16+,18+,19+,20-,21+,22-,23-,24-/m0/s1
SMILES	OC[C@H]1O[C@@H](O[C@@H]2OC=C[C@@H]3[C@H]2[C@@](C)(O)C[C@H]3OC(=O)/C=C/c2ccccc2)[C@@H]([C@H]([C@@H]1O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	478.18	Volume:	461.518 ? Van der Waals volume.
Dense:	1.036	LogP:	0.617 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.217 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.111 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	7.0	Rigid Bonds:	24.0
TPSA:	155.14 ? Topological Polar Surface Area.	H-Bond Acceptor:	10.0
H-Bond Donor:	5.0	Rings:	4.0
Heavy Atoms:	10.0

MedChem Properties

QED Drug-Likeness Score:	0.271	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.746	Fsp³:	0.542
MCE-18:	93.459 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.716	Fluc inhibitor:	0.666 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.107 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.071 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.279	Promiscuous compounds:	0.166

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.814	MDCK Permeability:	-5.187
Pgp-inhibitor:	0.015	Pgp-substrate:	0.15
PAMPA:	0.984 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.557
20% Bioavailability (F20%):	0.573	30% Bioavailability (F30%):	0.998
50% Bioavailability (F50%):	0.989

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.046	MRP1:	0.016
Plasma Protein Binding (PPB):	77.828%	Volume Distribution (VD):	-0.691
Fu:	22.398% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.002
BSEP inhibitor:	0.055

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.029
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.062
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.0 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

2.094

Half-life (T1/2):

2.499

ADMET: Toxicity

hERG Blockers:	0.032	hERG Blockers (10um):	0.135
Human Hepatotoxicity (H-HT):	0.644	Drug-induced Liver Injury (DILI):	0.814
AMES Toxicity:	0.929	Rat Oral Acute Toxicity:	0.017
Maximum Recommended Daily Dose:	0.064	Skin Sensitization:	1.0
Carcinogencity:	0.209	Eye Corrosion:	0.0
Eye Irritation:	0.206	Respiratory Toxicity:	0.012
Drug-induced Neurotoxicity:	0.093	Ototoxicity:	0.899
Hematotoxicity:	0.269	Drug-induced Nephrotoxicity:	0.849
Genotoxicity:	0.205	RPMI-8226 Immunitoxicity:	0.096
A549 Cytotoxicity:	0.342	Hek293 Cytotoxicity:	0.318
BCF:	0.638 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	3.272 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.008 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.266 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	Roots	n.a.	n.a.	PMID[22916954]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8101	Rehmannia glutinosa	Species	Orobanchaceae	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

Activity Type	# Activity
IC50	5

Activity Type	# Activity
Cell line	5

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
NPT179	Cell line	A2780	Homo sapiens	IC50	>	10000.0	nM	PMID[22500574]
NPT81	Cell line	A549	Homo sapiens	IC50	>	10000.0	nM	PMID[19105653]
NPT547	Cell line	BGC-823	Homo sapiens	IC50	>	10000.0	nM	PMID[22037378]
NPT181	Cell line	Bel-7402	Homo sapiens	IC50	>	10000.0	nM	DOI[10.1007/s00044-010-9321-6]
NPT180	Cell line	HCT-8	Homo sapiens	IC50	>	10000.0	nM	PMID[24893224]

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 NPC145287 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	9116
0.1-0.2	34645
0.2-0.3	5269
0.3-0.4	724
0.4-0.5	78
0.5-0.6	20
0.6-0.7	5
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
0.6429	Remote Similarity	NPC485190
0.6392	Remote Similarity	NPC208818
0.6235	Remote Similarity	NPC233500
0.6092	Remote Similarity	NPC196130
0.6	Remote Similarity	NPC479962
0.5977	Remote Similarity	NPC219656
0.5889	Remote Similarity	NPC163783
0.5882	Remote Similarity	NPC276047
0.5882	Remote Similarity	NPC267733
0.5795	Remote Similarity	NPC486495
0.5747	Remote Similarity	NPC46644
0.5714	Remote Similarity	NPC219804
0.5568	Remote Similarity	NPC18789
0.5556	Remote Similarity	NPC282551
0.5556	Remote Similarity	NPC485186
0.5556	Remote Similarity	NPC485187
0.5474	Remote Similarity	NPC161125
0.5326	Remote Similarity	NPC470685
0.5269	Remote Similarity	NPC89693
0.5213	Remote Similarity	NPC229548
0.5161	Remote Similarity	NPC322503
0.5109	Remote Similarity	NPC479970
0.5055	Remote Similarity	NPC49597
0.5053	Remote Similarity	NPC240592
0.5053	Remote Similarity	NPC117346

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC145287 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3337
0.1-0.2	5643
0.2-0.3	168
0.3-0.4	1
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