NPASS Compound

Natural Product: NPC508504

Natural Product ID	NPC508504
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Epiheterodendrin
IUPAC Name	(2~{R})-3-methyl-2-[(2~{R},3~{R},4~{S},5~{S},6~{R})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-butanenitrile
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 37 37 0 0 0 0 0 0 0 0999 V2000 2.4597 0.6257 -3.1592 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6186 0.6913 -1.6562 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0802 0.5382 -1.2555 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8155 -0.4519 -1.0260 C 0 0 2 0 0 0 0 0 0 0 0 0 2.3829 -1.6992 -1.5768 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8406 -2.6622 -1.9986 N 0 0 0 0 0 0 0 0 0 0 0 0 0.4793 -0.3102 -1.2907 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2766 -0.1793 -0.1557 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2153 -1.1999 0.0152 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6860 -1.1697 1.3228 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4370 -2.4294 1.6801 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5347 -2.6397 0.8720 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4944 0.0688 1.5252 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0377 0.1914 2.7767 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5384 1.2512 1.3322 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1364 2.4520 1.5943 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0574 1.1274 -0.1043 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3254 2.2064 -0.5179 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2828 1.6607 -3.5084 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5588 0.0147 -3.4024 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3735 0.1850 -3.6048 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2706 1.6392 -1.2307 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3568 -0.5298 -1.2065 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7463 1.0697 -1.9659 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2553 0.9701 -0.2580 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0792 -0.4397 0.0475 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3725 -0.2171 0.7614 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7910 -1.1063 1.9780 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7710 -3.3050 1.6117 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8062 -2.3471 2.7226 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1674 -1.8997 0.8636 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2680 0.1244 0.7098 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9033 0.6639 2.6890 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6601 1.0329 1.9792 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0589 2.4117 1.9084 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9737 1.0135 -0.7336 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1664 2.6480 0.2210 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 3 0 4 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 10 13 1 0 13 14 1 0 13 15 1 0 15 16 1 0 15 17 1 0 17 18 1 0 17 8 1 0 1 19 1 0 1 20 1 0 1 21 1 0 2 22 1 0 3 23 1 0 3 24 1 0 3 25 1 0 4 26 1 1 8 27 1 1 10 28 1 1 11 29 1 0 11 30 1 0 12 31 1 0 13 32 1 6 14 33 1 0 15 34 1 1 16 35 1 0 17 36 1 6 18 37 1 0 M END

Standard InCHIKey	CQWWASNOGSDPRL-OVHRRVLLSA-N
Standard InCHI	InChI=1S/C11H19NO6/c1-5(2)6(3-12)17-11-10(16)9(15)8(14)7(4-13)18-11/h5-11,13-16H,4H2,1-2H3/t6-,7+,8+,9-,10+,11+/m0/s1
SMILES	CC(C)[C@H](C#N)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	261.12	Volume:	248.721 ? Van der Waals volume.
Dense:	1.05	LogP:	-0.075 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.127 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-0.859 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	7.0
TPSA:	123.17 ? Topological Polar Surface Area.	H-Bond Acceptor:	7.0
H-Bond Donor:	4.0	Rings:	1.0
Heavy Atoms:	7.0

MedChem Properties

QED Drug-Likeness Score:	0.478	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.219	Fsp³:	0.909
MCE-18:	24.762 ? 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:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.189	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.018 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.444	Promiscuous compounds:	0.011

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.352	MDCK Permeability:	-4.777
Pgp-inhibitor:	0.417	Pgp-substrate:	0.556
PAMPA:	0.936 ? 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):	0.39
20% Bioavailability (F20%):	0.035	30% Bioavailability (F30%):	0.69
50% Bioavailability (F50%):	0.732

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.144
Plasma Protein Binding (PPB):	38.671%	Volume Distribution (VD):	-0.527
Fu:	60.246% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.999
OATP1B3 inhibitor:	0.989	BCRP inhibitor:	0.035
BSEP inhibitor:	0.016

ADMET: Metabolism

CYP1A2-inhibitor:	0.013	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.018	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.001	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.008
CYP3A4-inhibitor:	0.027	CYP3A4-substrate:	0.003
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.367
HLM stability:	0.089 ? 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):

2.333

Half-life (T1/2):

2.134

ADMET: Toxicity

hERG Blockers:	0.021	hERG Blockers (10um):	0.106
Human Hepatotoxicity (H-HT):	0.654	Drug-induced Liver Injury (DILI):	0.923
AMES Toxicity:	0.806	Rat Oral Acute Toxicity:	0.102
Maximum Recommended Daily Dose:	0.087	Skin Sensitization:	0.994
Carcinogencity:	0.128	Eye Corrosion:	0.056
Eye Irritation:	0.919	Respiratory Toxicity:	0.513
Drug-induced Neurotoxicity:	0.135	Ototoxicity:	0.88
Hematotoxicity:	0.425	Drug-induced Nephrotoxicity:	0.556
Genotoxicity:	0.771	RPMI-8226 Immunitoxicity:	0.081
A549 Cytotoxicity:	0.06	Hek293 Cytotoxicity:	0.13
BCF:	0.205 ? 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:	2.12 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.655 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	2.804 ? 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
NPO55702	Heterodendron oleaefolium	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO51902	Hordeum vulgare L. s.l. (H. vulgare L. s.str. and H. vulgare subsp. hexastichon (L.) Celak.)	Genus	Poaceae	Eukaryota	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

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 NPC508504 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	27255
0.1-0.2	18969
0.2-0.3	2879
0.3-0.4	612
0.4-0.5	124
0.5-0.6	8
0.6-0.7	10
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
0.6875	Remote Similarity	NPC23134
0.6389	Remote Similarity	NPC143326
0.6061	Remote Similarity	NPC42503
0.6061	Remote Similarity	NPC282143
0.6061	Remote Similarity	NPC107914
0.6061	Remote Similarity	NPC242073
0.6061	Remote Similarity	NPC299781
0.6061	Remote Similarity	NPC157193
0.6061	Remote Similarity	NPC608193
0.6	Remote Similarity	NPC124963
0.5789	Remote Similarity	NPC31496
0.5405	Remote Similarity	NPC326533
0.5366	Remote Similarity	NPC268243
0.5263	Remote Similarity	NPC317501
0.5263	Remote Similarity	NPC605930
0.525	Remote Similarity	NPC233726
0.5238	Remote Similarity	NPC323361
0.5111	Remote Similarity	NPC601741

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC508504 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7621
0.1-0.2	1377
0.2-0.3	120
0.3-0.4	15
0.4-0.5	13
0.5-0.6	4
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
0.5526	Remote Similarity	NPD905	Phase 4
0.5238	Remote Similarity	NPD889	Approved
0.5238	Remote Similarity	NPD894	Phase 4
0.5143	Remote Similarity	NPD8994	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