NPASS Compound

Natural Product: NPC90905

Natural Product ID	NPC90905
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Hyemaloside B
IUPAC Name	[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-[(4-hydroxybenzoyl)oxymethyl]-2-(4-hydroxyphenoxy)oxan-3-yl] 3,4,5-trihydroxybenzoate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL498793
PubChem CID	25110931
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0004165] Phenolic 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 63 66 0 0 0 0 0 0 0 0999 V2000 -0.5048 6.4671 3.1052 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5232 5.5112 2.0840 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4177 4.1762 2.3793 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4373 3.2330 1.3511 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5602 3.6071 0.0414 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6671 4.9690 -0.2498 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6482 5.9056 0.7654 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5847 2.7282 -1.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4960 1.3275 -0.9646 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6463 0.9651 -1.6340 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6632 -0.3036 -2.1737 C 0 0 2 0 0 0 0 0 0 0 0 0 1.9445 -0.5696 -2.9453 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1051 -0.4577 -2.1547 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3980 -1.2231 -1.0419 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5798 -2.1034 -0.6804 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6110 -1.0517 -0.2749 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5237 -0.0941 -0.6473 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7080 0.0944 0.0788 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9613 -0.6819 1.1709 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0615 -1.6461 1.5615 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8826 -1.8246 0.8282 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1554 -0.4626 1.8687 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5036 -0.6279 -3.0620 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5800 0.4172 -2.9766 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7564 0.7525 -1.5136 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2440 -0.3722 -0.8528 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4747 -0.4707 -0.2395 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2224 0.5094 -0.2666 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8207 -1.7273 0.4060 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9678 -2.8073 0.4113 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3087 -3.9999 1.0358 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4379 -5.0735 1.0300 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5234 -4.1381 1.6746 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3671 -3.0487 1.6610 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0348 -1.8591 1.0418 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6003 -3.1424 2.2916 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8732 -5.3420 2.3079 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2714 1.5354 -3.7371 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0253 -1.8681 -2.7719 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8384 7.4042 2.8932 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3203 3.8889 3.4253 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3514 2.2198 1.6590 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7667 5.3344 -1.2624 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7310 6.9696 0.5587 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3821 1.0151 0.0808 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6425 -1.0226 -1.3310 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0673 0.1522 -3.7840 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8915 -1.5675 -3.4025 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2926 0.5057 -1.5201 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3887 0.8699 -0.2683 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2727 -2.2505 2.4233 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2051 -2.5974 1.1757 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0022 -0.7614 1.4039 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1644 -0.6532 -4.1173 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5263 -0.0186 -3.3465 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5427 1.5341 -1.4580 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9949 -2.7097 -0.0954 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0241 -5.4565 1.8643 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7232 -1.0002 1.0419 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7205 -3.5499 3.2062 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8906 -5.5142 2.3198 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6473 2.1451 -3.2894 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5283 -2.2405 -2.0011 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 2 0 5 6 1 0 6 7 2 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 14 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 19 22 1 0 11 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 2 0 27 29 1 0 29 30 2 0 30 31 1 0 31 32 1 0 31 33 2 0 33 34 1 0 34 35 2 0 34 36 1 0 33 37 1 0 24 38 1 0 23 39 1 0 7 2 1 0 25 9 1 0 35 29 1 0 21 16 1 0 1 40 1 0 3 41 1 0 4 42 1 0 6 43 1 0 7 44 1 0 9 45 1 1 11 46 1 1 12 47 1 0 12 48 1 0 17 49 1 0 18 50 1 0 20 51 1 0 21 52 1 0 22 53 1 0 23 54 1 6 24 55 1 6 25 56 1 6 30 57 1 0 32 58 1 0 35 59 1 0 36 60 1 0 37 61 1 0 38 62 1 0 39 63 1 0 M END

Standard InCHIKey	LIANLIDDEFJTSX-XZWSAFPPSA-N
Standard InCHI	InChI=1S/C26H24O13/c27-14-3-1-12(2-4-14)24(34)36-11-19-21(32)22(33)23(26(38-19)37-16-7-5-15(28)6-8-16)39-25(35)13-9-17(29)20(31)18(30)10-13/h1-10,19,21-23,26-33H,11H2/t19-,21-,22+,23-,26-/m1/s1
SMILES	Oc1ccc(cc1)O[C@@H]1O[C@H](COC(=O)c2ccc(cc2)O)[C@H]([C@@H]([C@H]1OC(=O)c1cc(O)c(c(c1)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	544.12	Volume:	509.298 ? Van der Waals volume.
Dense:	1.068	LogP:	1.345 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.614 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.124 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	9.0	Rigid Bonds:	26.0
TPSA:	212.67 ? Topological Polar Surface Area.	H-Bond Acceptor:	13.0
H-Bond Donor:	7.0	Rings:	4.0
Heavy Atoms:	13.0

MedChem Properties

QED Drug-Likeness Score:	0.164	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.887	Fsp³:	0.231
MCE-18:	89.438 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	1	PAINS Alert:	1
Colloidal aggregators:	0.683	Fluc inhibitor:	0.472 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.065 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.589 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.421	Promiscuous compounds:	0.965

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.506	MDCK Permeability:	-5.002
Pgp-inhibitor:	0.0	Pgp-substrate:	0.005
PAMPA:	0.997 ? 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):	0.0
20% Bioavailability (F20%):	0.7	30% Bioavailability (F30%):	0.914
50% Bioavailability (F50%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.995
Plasma Protein Binding (PPB):	87.452%	Volume Distribution (VD):	-0.284
Fu:	13.194% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.999	BCRP inhibitor:	0.096
BSEP inhibitor:	0.408

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.003
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.582
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.998
HLM stability:	0.141 ? 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):

6.221

Half-life (T1/2):

2.241

ADMET: Toxicity

hERG Blockers:	0.094	hERG Blockers (10um):	0.917
Human Hepatotoxicity (H-HT):	0.054	Drug-induced Liver Injury (DILI):	0.693
AMES Toxicity:	0.375	Rat Oral Acute Toxicity:	0.034
Maximum Recommended Daily Dose:	0.256	Skin Sensitization:	1.0
Carcinogencity:	0.311	Eye Corrosion:	0.0
Eye Irritation:	0.948	Respiratory Toxicity:	0.02
Drug-induced Neurotoxicity:	0.003	Ototoxicity:	0.813
Hematotoxicity:	0.001	Drug-induced Nephrotoxicity:	0.008
Genotoxicity:	0.789	RPMI-8226 Immunitoxicity:	0.006
A549 Cytotoxicity:	0.966	Hek293 Cytotoxicity:	0.691
BCF:	0.849 ? 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:	3.79 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.623 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.286 ? 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
NPO27524	Eugenia hyemalis	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18763827]
NPO27524	Eugenia hyemalis	Species	Myrtaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[18763827]
NPO27524	Eugenia hyemalis	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27524	Eugenia hyemalis	Species	Myrtaceae	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	3

Activity Type	# Activity
Others	3

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	>	18300.0	nM	PMID[25710081]
NPT2	Others	Unspecified	n.a.	IC50	=	3320.0	nM	PMID[15711537]
NPT2	Others	Unspecified	n.a.	IC50	=	2440.0	nM	PMID[26005918]

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 NPC90905 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	15329
0.1-0.2	30015
0.2-0.3	4116
0.3-0.4	309
0.4-0.5	65
0.5-0.6	16
0.6-0.7	4
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	Natural Product ID
0.931	High Similarity	NPC4013
0.7031	Intermediate Similarity	NPC74319
0.6765	Remote Similarity	NPC198125
0.6765	Remote Similarity	NPC95421
0.625	Remote Similarity	NPC93619
0.619	Remote Similarity	NPC44260
0.5795	Remote Similarity	NPC603079
0.5618	Remote Similarity	NPC97119
0.5571	Remote Similarity	NPC65833
0.5405	Remote Similarity	NPC472859
0.5375	Remote Similarity	NPC289346
0.5352	Remote Similarity	NPC287872
0.5333	Remote Similarity	NPC25389
0.527	Remote Similarity	NPC166277
0.5227	Remote Similarity	NPC470438
0.5205	Remote Similarity	NPC484156
0.5185	Remote Similarity	NPC70804
0.5156	Remote Similarity	NPC226738
0.5132	Remote Similarity	NPC140151
0.5075	Remote Similarity	NPC482667
0.5055	Remote Similarity	NPC280385
0.5055	Remote Similarity	NPC475183

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC90905 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3901
0.1-0.2	5098
0.2-0.3	147
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