NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	177.1
Volume:	167.23
LogP:	-1.844
LogD:	-2.072
LogS:	0.075
# Rotatable Bonds:	1
TPSA:	84.16
# H-Bond Aceptor:	5
# H-Bond Donor:	4
# Rings:	1
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.352
Synthetic Accessibility Score:	3.969
Fsp3:	1.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.214
MDCK Permeability:	0.000235537881962955
Pgp-inhibitor:	0.001
Pgp-substrate:	0.623
Human Intestinal Absorption (HIA):	0.712
20% Bioavailability (F20%):	0.046
30% Bioavailability (F30%):	0.944

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.254
Plasma Protein Binding (PPB):	11.487650871276855%
Volume Distribution (VD):	0.445
Pgp-substrate:	88.86522674560547%

ADMET: Metabolism

CYP1A2-inhibitor:	0.022
CYP1A2-substrate:	0.08
CYP2C19-inhibitor:	0.016
CYP2C19-substrate:	0.845
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.213
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.39
CYP3A4-inhibitor:	0.002
CYP3A4-substrate:	0.042

ADMET: Excretion

Clearance (CL):	2.475
Half-life (T1/2):	0.793

ADMET: Toxicity

hERG Blockers:	0.061
Human Hepatotoxicity (H-HT):	0.142
Drug-inuced Liver Injury (DILI):	0.042
AMES Toxicity:	0.055
Rat Oral Acute Toxicity:	0.014
Maximum Recommended Daily Dose:	0.006
Skin Sensitization:	0.203
Carcinogencity:	0.037
Eye Corrosion:	0.266
Eye Irritation:	0.357
Respiratory Toxicity:	0.803

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC170172

Natural Product ID:	NPC170172
*Common Name:**	N-Methyl-1-Deoxynojirimycin
IUPAC Name:	(2R,3R,4R,5S)-2-(hydroxymethyl)-1-methylpiperidine-3,4,5-triol
Synonyms:
Standard InCHIKey:	AAKDPDFZMNYDLR-XZBKPIIZSA-N
Standard InCHI:	InChI=1S/C7H15NO4/c1-8-2-5(10)7(12)6(11)4(8)3-9/h4-7,9-12H,2-3H2,1H3/t4-,5+,6-,7-/m1/s1
SMILES:	OC[C@H]1N(C)C[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL75971
PubChem CID:	92381
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000195] Piperidines

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20815207]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[21319773]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	leaf	n.a.	PMID[21319773]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	bark	n.a.	PMID[21319773]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	leaf	n.a.	PMID[22207282]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[23806866]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	root bark	University of Veterinary and Pharmaceutical Sciences Brno (UVPS Brno), Brno, Czech Republic	2011-APR	PMID[24901948]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	Konya, Turkey	2007-APR	PMID[24901948]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	leaves	Chungbuk, Korea	n.a.	PMID[25935644]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[25981820]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	latex	n.a.	PMID[27294120]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	Root barks	n.a.	n.a.	PMID[3097265]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28265	Morus alba	Species	Moraceae	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	NP ID	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
EC50	3
IC50	11
Ki	4
Others	5

Activity Type	# Activity
Cell Line	4
Individual Protein	12
Organism	1
Others	6

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT497	Individual Protein	Maltase-glucoamylase	Homo sapiens	IC50	=	120.0	nM	PMID[532282]
NPT462	Individual Protein	Sucrase-isomaltase	Rattus norvegicus	IC50	=	40.0	nM	PMID[532282]
NPT462	Individual Protein	Sucrase-isomaltase	Rattus norvegicus	IC50	=	4400.0	nM	PMID[532282]
NPT1050	Individual Protein	Trehalase	Rattus norvegicus	IC50	=	28000.0	nM	PMID[532282]
NPT1051	Individual Protein	Lactase-glycosylceramidase	Rattus norvegicus	IC50	=	4400.0	nM	PMID[532282]
NPT1052	Individual Protein	Mannosidase 2 alpha 1	Rattus norvegicus	IC50	<	50000.0	nM	PMID[532282]
NPT1053	Individual Protein	Alpha-mannosidase 2C1	Rattus norvegicus	IC50	=	500000.0	nM	PMID[532282]
NPT1054	Individual Protein	Mannosidase 2, alpha B1	Rattus norvegicus	IC50	=	1000000.0	nM	PMID[532282]
NPT1052	Individual Protein	Mannosidase 2 alpha 1	Rattus norvegicus	Ki	<	50000.0	nM	PMID[532282]
NPT25	Cell Line	MT4	Homo sapiens	EC50	=	69000.0	ug.mL-1	PMID[532282]
NPT25	Cell Line	MT4	Homo sapiens	CC50	>	100000.0	ug.mL-1	PMID[532282]
NPT112	Cell Line	MOLT-4	Homo sapiens	EC50	=	100000.0	ug.mL-1	PMID[532282]
NPT112	Cell Line	MOLT-4	Homo sapiens	CC50	>	100000.0	ug.mL-1	PMID[532282]
NPT462	Individual Protein	Sucrase-isomaltase	Rattus norvegicus	Ki	=	20.0	nM	PMID[532283]
NPT60	Individual Protein	Lysosomal alpha-glucosidase	Homo sapiens	Ki	=	420.0	nM	PMID[532283]
NPT5895	Individual Protein	Lysosomal alpha-glucosidase	Mus musculus	EC50	=	74500.0	nM	PMID[532285]
NPT2	Others	Unspecified		IC50	=	120000.0	nM	PMID[532282]
NPT2	Others	Unspecified		IC50	=	20000.0	nM	PMID[532282]
NPT2	Others	Unspecified		IC50	=	1500.0	nM	PMID[532282]
NPT2	Others	Unspecified		Ki	=	5800.0	nM	PMID[532282]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	T1/2	=	1.7	hr	PMID[532283]
NPT27	Others	Unspecified		T1/2	=	3.5	hr	PMID[532283]
NPT2	Others	Unspecified		Ratio	=	21.0	n.a.	PMID[532283]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC170172 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	157
0.1-0.2	15417
0.2-0.3	21140
0.3-0.4	4767
0.4-0.5	867
0.5-0.6	230
0.6-0.7	69
0.7-0.8	18
0.8-0.85	13
0.85-0.9	16
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.931	High Similarity	NPC163134
0.931	High Similarity	NPC471419
0.8814	High Similarity	NPC69669
0.8814	High Similarity	NPC22774
0.8814	High Similarity	NPC306462
0.8814	High Similarity	NPC2432
0.8814	High Similarity	NPC218150
0.8814	High Similarity	NPC150680
0.8689	High Similarity	NPC303798
0.8689	High Similarity	NPC286851
0.8621	High Similarity	NPC233364
0.8621	High Similarity	NPC471421
0.8525	High Similarity	NPC223386
0.8525	High Similarity	NPC471892
0.8525	High Similarity	NPC471780
0.8525	High Similarity	NPC198341
0.8525	High Similarity	NPC75435
0.8525	High Similarity	NPC142290
0.8413	Intermediate Similarity	NPC34291
0.8413	Intermediate Similarity	NPC126664
0.8387	Intermediate Similarity	NPC315980
0.8305	Intermediate Similarity	NPC290106
0.8305	Intermediate Similarity	NPC143809
0.8305	Intermediate Similarity	NPC76726
0.8305	Intermediate Similarity	NPC193593
0.8281	Intermediate Similarity	NPC268922
0.8136	Intermediate Similarity	NPC204709
0.8125	Intermediate Similarity	NPC471418
0.803	Intermediate Similarity	NPC476695
0.803	Intermediate Similarity	NPC476696
0.803	Intermediate Similarity	NPC476694
0.7937	Intermediate Similarity	NPC233034
0.7761	Intermediate Similarity	NPC299603
0.7761	Intermediate Similarity	NPC285014
0.7761	Intermediate Similarity	NPC255535
0.7761	Intermediate Similarity	NPC137554
0.7761	Intermediate Similarity	NPC28959
0.7627	Intermediate Similarity	NPC275727
0.7576	Intermediate Similarity	NPC171850
0.75	Intermediate Similarity	NPC150557
0.7353	Intermediate Similarity	NPC163538
0.7353	Intermediate Similarity	NPC115800
0.7297	Intermediate Similarity	NPC471420
0.7273	Intermediate Similarity	NPC116377
0.7273	Intermediate Similarity	NPC77191
0.7273	Intermediate Similarity	NPC101746
0.7273	Intermediate Similarity	NPC473952
0.7273	Intermediate Similarity	NPC69798
0.7206	Intermediate Similarity	NPC475127
0.7206	Intermediate Similarity	NPC475715
0.7206	Intermediate Similarity	NPC473419
0.7188	Intermediate Similarity	NPC30126
0.7188	Intermediate Similarity	NPC62507
0.7188	Intermediate Similarity	NPC57846
0.7188	Intermediate Similarity	NPC474014
0.7188	Intermediate Similarity	NPC8087
0.7167	Intermediate Similarity	NPC178263
0.7167	Intermediate Similarity	NPC277072
0.7121	Intermediate Similarity	NPC472609
0.7121	Intermediate Similarity	NPC474928
0.7101	Intermediate Similarity	NPC473710
0.7101	Intermediate Similarity	NPC475694
0.7059	Intermediate Similarity	NPC474469
0.7059	Intermediate Similarity	NPC266242
0.7059	Intermediate Similarity	NPC254617
0.7059	Intermediate Similarity	NPC306763
0.7059	Intermediate Similarity	NPC74555
0.7027	Intermediate Similarity	NPC98750
0.7015	Intermediate Similarity	NPC294883
0.7015	Intermediate Similarity	NPC12514
0.6933	Remote Similarity	NPC70574
0.6912	Remote Similarity	NPC141156
0.6912	Remote Similarity	NPC59221
0.6912	Remote Similarity	NPC184150
0.6857	Remote Similarity	NPC223174
0.6857	Remote Similarity	NPC327753
0.6857	Remote Similarity	NPC327486
0.6825	Remote Similarity	NPC311668
0.6825	Remote Similarity	NPC65832
0.6825	Remote Similarity	NPC10262
0.6753	Remote Similarity	NPC271772
0.6753	Remote Similarity	NPC36927
0.6667	Remote Similarity	NPC474468
0.6667	Remote Similarity	NPC322801
0.6667	Remote Similarity	NPC129100
0.6667	Remote Similarity	NPC291650
0.6625	Remote Similarity	NPC469363
0.6623	Remote Similarity	NPC219340
0.6562	Remote Similarity	NPC293551
0.6494	Remote Similarity	NPC100204
0.6494	Remote Similarity	NPC83248
0.6447	Remote Similarity	NPC314968
0.6447	Remote Similarity	NPC314772
0.6349	Remote Similarity	NPC272396
0.6338	Remote Similarity	NPC107224
0.6324	Remote Similarity	NPC145627
0.6308	Remote Similarity	NPC8979
0.625	Remote Similarity	NPC165119
0.6154	Remote Similarity	NPC316807
0.6133	Remote Similarity	NPC315806
0.6081	Remote Similarity	NPC306973
0.6027	Remote Similarity	NPC23721
0.6	Remote Similarity	NPC471423
0.6	Remote Similarity	NPC185084
0.6	Remote Similarity	NPC471442
0.5965	Remote Similarity	NPC266553
0.5952	Remote Similarity	NPC306838
0.5926	Remote Similarity	NPC192065
0.5926	Remote Similarity	NPC293908
0.5926	Remote Similarity	NPC86412
0.5926	Remote Similarity	NPC66052
0.5926	Remote Similarity	NPC325034
0.5915	Remote Similarity	NPC160661
0.5897	Remote Similarity	NPC329077
0.589	Remote Similarity	NPC195165
0.5889	Remote Similarity	NPC313821
0.5882	Remote Similarity	NPC319991
0.5873	Remote Similarity	NPC224624
0.5846	Remote Similarity	NPC270041
0.5844	Remote Similarity	NPC470993
0.5844	Remote Similarity	NPC470992
0.5821	Remote Similarity	NPC471605
0.5821	Remote Similarity	NPC471443
0.5769	Remote Similarity	NPC244539
0.5769	Remote Similarity	NPC477002
0.5714	Remote Similarity	NPC112398
0.5698	Remote Similarity	NPC52533
0.5696	Remote Similarity	NPC313762
0.5692	Remote Similarity	NPC123814
0.569	Remote Similarity	NPC99573
0.569	Remote Similarity	NPC102981
0.569	Remote Similarity	NPC88278
0.569	Remote Similarity	NPC111882
0.569	Remote Similarity	NPC227707
0.5679	Remote Similarity	NPC318258
0.5676	Remote Similarity	NPC316445
0.5667	Remote Similarity	NPC320240
0.5667	Remote Similarity	NPC70756
0.5658	Remote Similarity	NPC477200
0.5645	Remote Similarity	NPC321087
0.5645	Remote Similarity	NPC277475
0.5645	Remote Similarity	NPC81384
0.5634	Remote Similarity	NPC17455
0.5625	Remote Similarity	NPC27359
0.5625	Remote Similarity	NPC295832
0.5625	Remote Similarity	NPC198398

Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC170172 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	84
0.1-0.2	3719
0.2-0.3	3920
0.3-0.4	1031
0.4-0.5	260
0.5-0.6	103
0.6-0.7	21
0.7-0.8	5
0.8-0.85	1
0.85-0.9	4
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9643	High Similarity	NPD393	Approved
0.9464	High Similarity	NPD9455	Approved
0.8814	High Similarity	NPD9026	Phase 2
0.8814	High Similarity	NPD9027	Phase 3
0.8814	High Similarity	NPD9029	Phase 3
0.8814	High Similarity	NPD9028	Phase 2
0.8413	Intermediate Similarity	NPD9443	Clinical (unspecified phase)
0.7937	Intermediate Similarity	NPD9440	Discontinued
0.7581	Intermediate Similarity	NPD9239	Approved
0.7581	Intermediate Similarity	NPD9240	Approved
0.7313	Intermediate Similarity	NPD9444	Discontinued
0.7105	Intermediate Similarity	NPD882	Phase 2
0.7105	Intermediate Similarity	NPD883	Phase 2
0.6923	Remote Similarity	NPD9024	Phase 2
0.6923	Remote Similarity	NPD9022	Phase 2
0.6901	Remote Similarity	NPD6704	Discontinued
0.6857	Remote Similarity	NPD9445	Approved
0.6757	Remote Similarity	NPD372	Clinical (unspecified phase)
0.6709	Remote Similarity	NPD9401	Discovery
0.6667	Remote Similarity	NPD9030	Approved
0.6667	Remote Similarity	NPD9031	Approved
0.6667	Remote Similarity	NPD9033	Approved
0.6667	Remote Similarity	NPD9032	Approved
0.6447	Remote Similarity	NPD9435	Approved
0.6447	Remote Similarity	NPD9434	Approved
0.6232	Remote Similarity	NPD9211	Clinical (unspecified phase)
0.6143	Remote Similarity	NPD1457	Discontinued
0.6133	Remote Similarity	NPD9034	Approved
0.6133	Remote Similarity	NPD9653	Clinical (unspecified phase)
0.6133	Remote Similarity	NPD67	Phase 2
0.6024	Remote Similarity	NPD394	Phase 3
0.5942	Remote Similarity	NPD3192	Approved
0.5942	Remote Similarity	NPD3193	Approved
0.5926	Remote Similarity	NPD9051	Approved
0.5926	Remote Similarity	NPD9053	Approved
0.5926	Remote Similarity	NPD9052	Approved
0.5889	Remote Similarity	NPD3191	Approved
0.5889	Remote Similarity	NPD3189	Approved
0.5889	Remote Similarity	NPD3190	Approved
0.5867	Remote Similarity	NPD9446	Approved
0.5821	Remote Similarity	NPD6439	Phase 3
0.5769	Remote Similarity	NPD9407	Approved
0.5765	Remote Similarity	NPD241	Discontinued
0.5714	Remote Similarity	NPD361	Discontinued
0.5714	Remote Similarity	NPD355	Phase 2
0.5692	Remote Similarity	NPD9668	Phase 2
0.5692	Remote Similarity	NPD3215	Phase 1
0.569	Remote Similarity	NPD8996	Phase 3
0.569	Remote Similarity	NPD8995	Clinical (unspecified phase)
0.5672	Remote Similarity	NPD6706	Discontinued
0.5645	Remote Similarity	NPD9462	Approved
0.5645	Remote Similarity	NPD9463	Phase 3
0.5625	Remote Similarity	NPD9226	Approved
0.5625	Remote Similarity	NPD9225	Phase 3

Bioactivity similarity: Similar Natural Products in NPASS

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