NPASS Compound

Natural Product: NPC268922

Natural Product ID	NPC268922
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Beta-1-C-Ethyl-1-Deoxymannojirimycin
IUPAC Name	(2S,3R,4R,5R,6R)-2-ethyl-6-(hydroxymethyl)piperidine-3,4,5-triol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL376799
PubChem CID	14446759
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000195] Piperidines

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 30 30 0 0 0 0 0 0 0 0999 V2000 2.8902 1.4773 0.1213 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3886 0.0542 0.3481 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0416 -0.1005 -0.3469 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5643 -1.5016 -0.1144 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8863 -1.7070 -0.4788 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6637 -0.6060 0.2486 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1779 0.6826 -0.3791 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1183 1.8282 -0.1194 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6781 3.0003 -0.6841 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1460 0.9115 0.1486 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.0135 -0.7805 0.1864 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2893 -2.9639 -0.1111 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7376 -1.8974 1.1934 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3560 2.1973 0.7547 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9785 1.5646 0.3091 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6825 1.7483 -0.9349 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3240 -0.1321 1.4210 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1500 -0.6177 -0.1023 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1857 0.0495 -1.4310 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1648 -2.1723 -0.7636 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0196 -1.4937 -1.5730 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3192 -0.6805 1.3195 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0892 0.5558 -1.4866 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0886 1.5630 -0.5941 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3309 1.9243 0.9715 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6885 3.0579 -0.4961 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1311 0.9903 1.1782 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4050 -0.6654 1.0871 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2078 -3.5494 -0.9273 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2351 -2.7371 1.2554 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 7 10 1 0 6 11 1 0 5 12 1 0 4 13 1 0 10 3 1 0 1 14 1 0 1 15 1 0 1 16 1 0 2 17 1 0 2 18 1 0 3 19 1 6 4 20 1 6 5 21 1 6 6 22 1 1 7 23 1 6 8 24 1 0 8 25 1 0 9 26 1 0 10 27 1 0 11 28 1 0 12 29 1 0 13 30 1 0 M END

Standard InCHIKey	AFRPVDHJWCJLNM-SLBCVNJHSA-N
Standard InCHI	InChI=1S/C8H17NO4/c1-2-4-6(11)8(13)7(12)5(3-10)9-4/h4-13H,2-3H2,1H3/t4-,5+,6+,7+,8+/m0/s1
SMILES	CC[C@H]1[C@H]([C@H]([C@@H]([C@@H](CO)N1)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	191.12	Volume:	184.526 ? Van der Waals volume.
Dense:	1.036	LogP:	-0.812 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-0.467 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-0.279 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	2.0	Rigid Bonds:	6.0
TPSA:	92.95 ? Topological Polar Surface Area.	H-Bond Acceptor:	5.0
H-Bond Donor:	5.0	Rings:	1.0
Heavy Atoms:	5.0

MedChem Properties

QED Drug-Likeness Score:	0.342	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.149	Fsp³:	1.0
MCE-18:	21.0 ? 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:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.123	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.045 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.003 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.117	Promiscuous compounds:	0.259

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.321	MDCK Permeability:	-4.773
Pgp-inhibitor:	0.001	Pgp-substrate:	0.979
PAMPA:	0.902 ? 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):	0.943
20% Bioavailability (F20%):	0.956	30% Bioavailability (F30%):	0.994
50% Bioavailability (F50%):	0.979

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.021	MRP1:	0.364
Plasma Protein Binding (PPB):	19.045%	Volume Distribution (VD):	-0.39
Fu:	81.135% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.194
OATP1B3 inhibitor:	0.416	BCRP inhibitor:	0.018
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.004
CYP2C9-inhibitor:	0.207	CYP2C9-substrate:	0.004
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.03
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.695
HLM stability:	0.189 ? 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):

4.322

Half-life (T1/2):

2.137

ADMET: Toxicity

hERG Blockers:	0.028	hERG Blockers (10um):	0.216
Human Hepatotoxicity (H-HT):	0.426	Drug-induced Liver Injury (DILI):	0.175
AMES Toxicity:	0.64	Rat Oral Acute Toxicity:	0.097
Maximum Recommended Daily Dose:	0.022	Skin Sensitization:	0.933
Carcinogencity:	0.266	Eye Corrosion:	0.054
Eye Irritation:	0.876	Respiratory Toxicity:	0.16
Drug-induced Neurotoxicity:	0.049	Ototoxicity:	0.76
Hematotoxicity:	0.499	Drug-induced Nephrotoxicity:	0.651
Genotoxicity:	0.08	RPMI-8226 Immunitoxicity:	0.078
A549 Cytotoxicity:	0.096	Hek293 Cytotoxicity:	0.081
BCF:	0.258 ? 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:	2.141 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.534 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	2.782 ? 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
NPO7198	Scilla socialis	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17536859]
NPO7198	Scilla socialis	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7198	Scilla socialis	Species	Hyacinthaceae	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	4
Inhibition	4

Activity Type	# Activity
Individual protein	4
Others	4

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT509	Individual protein	Beta-galactosidase	Bos taurus	IC50	=	86000.0	nM	PMID[26042639]
NPT6343	Individual protein	Beta-galactosidase	Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903)	IC50	=	51000.0	nM	PMID[23234407]
NPT507	Individual protein	Alpha-galactosidase	Coffea arabica	Inhibition	<	50.0	%	PMID[18500841]
NPT503	Individual protein	Alpha-L-fucosidase I	Homo sapiens	IC50	=	83000.0	nM	Open TG-GATES in vivo data: Hematology

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified	n.a.	Inhibition	<	50.0	%	PMID[8691203]
NPT2	Others	Unspecified	n.a.	IC50	=	94000.0	nM	PMID[18341287]

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 NPC268922 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	40848
0.1-0.2	8824
0.2-0.3	134
0.3-0.4	25
0.4-0.5	12
0.5-0.6	3
0.6-0.7	9
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
0.6667	Remote Similarity	NPC223386
0.6667	Remote Similarity	NPC75435
0.6667	Remote Similarity	NPC142290
0.6667	Remote Similarity	NPC198341
0.6667	Remote Similarity	NPC471892
0.6667	Remote Similarity	NPC471780
0.6296	Remote Similarity	NPC286851
0.6296	Remote Similarity	NPC303798
0.6061	Remote Similarity	NPC471418
0.5517	Remote Similarity	NPC473710
0.5172	Remote Similarity	NPC116377
0.5172	Remote Similarity	NPC69798

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC268922 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8136
0.1-0.2	975
0.2-0.3	31
0.3-0.4	5
0.4-0.5	3
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