NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	147.09
Volume:	141.143
LogP:	-1.54
LogD:	-1.406
LogS:	0.047
# Rotatable Bonds:	0
TPSA:	72.72
# H-Bond Aceptor:	4
# H-Bond Donor:	4
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.322
Synthetic Accessibility Score:	4.048
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:	-5.08
MDCK Permeability:	0.00011167647608090192
Pgp-inhibitor:	0.0
Pgp-substrate:	0.82
Human Intestinal Absorption (HIA):	0.83
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.029

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.193
Plasma Protein Binding (PPB):	12.082998275756836%
Volume Distribution (VD):	0.678
Pgp-substrate:	88.3880844116211%

ADMET: Metabolism

CYP1A2-inhibitor:	0.024
CYP1A2-substrate:	0.068
CYP2C19-inhibitor:	0.038
CYP2C19-substrate:	0.734
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.158
CYP2D6-inhibitor:	0.011
CYP2D6-substrate:	0.655
CYP3A4-inhibitor:	0.002
CYP3A4-substrate:	0.046

ADMET: Excretion

Clearance (CL):	3.434
Half-life (T1/2):	0.668

ADMET: Toxicity

hERG Blockers:	0.022
Human Hepatotoxicity (H-HT):	0.39
Drug-inuced Liver Injury (DILI):	0.037
AMES Toxicity:	0.032
Rat Oral Acute Toxicity:	0.373
Maximum Recommended Daily Dose:	0.066
Skin Sensitization:	0.352
Carcinogencity:	0.094
Eye Corrosion:	0.032
Eye Irritation:	0.205
Respiratory Toxicity:	0.849

Download Data

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

Natural Product: NPC204709

Natural Product ID:	NPC204709
*Common Name:**	Deoxyfuconojirimycin
IUPAC Name:	(2S,3R,4S,5R)-2-methylpiperidine-3,4,5-triol
Synonyms:
Standard InCHIKey:	VYOCYWDJTQRZLC-KCDKBNATSA-N
Standard InCHI:	InChI=1S/C6H13NO3/c1-3-5(9)6(10)4(8)2-7-3/h3-10H,2H2,1H3/t3-,4+,5+,6-/m0/s1
SMILES:	C[C@H]1[C@H]([C@H]([C@@H](CN1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL314772
PubChem CID:	122618
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]
NPO8990	Fusarium proliferatum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23832252]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	Konya, Turkey	2007-APR	PMID[24901948]
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	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]
NPO8990	Fusarium proliferatum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27984201]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	Root barks	n.a.	n.a.	PMID[3097265]
NPO8990	Fusarium proliferatum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8991945]
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]
NPO8990	Fusarium proliferatum	Species	Nectriaceae	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
IC50	6
Ki	11
Others	11

Activity Type	# Activity
Individual Protein	20
Others	8

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT503	Individual Protein	Alpha-L-fucosidase I	Homo sapiens	Ki	=	80.0	nM	PMID[453279]
NPT503	Individual Protein	Alpha-L-fucosidase I	Homo sapiens	Ki	=	6.2	nM	PMID[453280]
NPT503	Individual Protein	Alpha-L-fucosidase I	Homo sapiens	Ki	=	6.2	nM	PMID[453281]
NPT503	Individual Protein	Alpha-L-fucosidase I	Homo sapiens	IC50	=	410.0	nM	PMID[453282]
NPT503	Individual Protein	Alpha-L-fucosidase I	Homo sapiens	Ki	=	31.0	nM	PMID[453282]
NPT503	Individual Protein	Alpha-L-fucosidase I	Homo sapiens	Ki	=	29.0	nM	PMID[453283]
NPT5152	Individual Protein	Alpha-L-fucosidase 2	Homo sapiens	Ki	=	9.8	nM	PMID[453284]
NPT503	Individual Protein	Alpha-L-fucosidase I	Homo sapiens	Ki	=	6.2	nM	PMID[453284]
NPT503	Individual Protein	Alpha-L-fucosidase I	Homo sapiens	Inhibition	=	99.0	%	PMID[453284]
NPT501	Individual Protein	Alpha-galactosidase A	Homo sapiens	Inhibition	=	74.0	%	PMID[453284]
NPT496	Individual Protein	Alpha-L-fucosidase 1	Bos taurus	Ki	=	1.7	nM	PMID[453285]
NPT496	Individual Protein	Alpha-L-fucosidase 1	Bos taurus	Ki	=	3.0	nM	PMID[453286]
NPT496	Individual Protein	Alpha-L-fucosidase 1	Bos taurus	IC50	=	5.0	nM	PMID[453286]
NPT503	Individual Protein	Alpha-L-fucosidase I	Homo sapiens	Ki	=	10.0	nM	PMID[453287]
NPT496	Individual Protein	Alpha-L-fucosidase 1	Bos taurus	Ki	=	3.0	nM	PMID[453288]
NPT509	Individual Protein	Beta-galactosidase	Bos taurus	Inhibition	=	3.7	%	PMID[453289]
NPT1131	Individual Protein	Alpha-galactosidase	Coffea arabica	Inhibition	=	5.2	%	PMID[453289]
NPT503	Individual Protein	Alpha-L-fucosidase I	Homo sapiens	IC50	=	140.0	nM	PMID[453289]
NPT5153	Individual Protein	Alpha-L-fucosidase I	Rattus norvegicus	IC50	=	340.0	nM	PMID[453289]
NPT496	Individual Protein	Alpha-L-fucosidase 1	Bos taurus	IC50	=	110.0	nM	PMID[453289]
NPT2	Others	Unspecified		IC50	=	3500000.0	nM	PMID[453278]
NPT2	Others	Unspecified		Inhibition	=	83.0	%	PMID[453284]
NPT2	Others	Unspecified		Inhibition	=	50.0	%	PMID[453284]
NPT2	Others	Unspecified		Inhibition	=	7.4	%	PMID[453289]
NPT2	Others	Unspecified		Inhibition	=	2.3	%	PMID[453289]
NPT2	Others	Unspecified		Inhibition	=	4.9	%	PMID[453289]
NPT2	Others	Unspecified		Inhibition	=	2.6	%	PMID[453289]
NPT2	Others	Unspecified		Inhibition	=	5.7	%	PMID[453289]

☑ 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 NPC204709 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	137
0.1-0.2	20992
0.2-0.3	18090
0.3-0.4	2538
0.4-0.5	638
0.5-0.6	187
0.6-0.7	57
0.7-0.8	31
0.8-0.85	5
0.85-0.9	16
0.9-0.95	5
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9455	High Similarity	NPC193593
0.9455	High Similarity	NPC290106
0.9455	High Similarity	NPC143809
0.9455	High Similarity	NPC76726
0.8966	High Similarity	NPC69669
0.8966	High Similarity	NPC306462
0.8966	High Similarity	NPC150680
0.8966	High Similarity	NPC22774
0.8966	High Similarity	NPC2432
0.8966	High Similarity	NPC218150
0.8833	High Similarity	NPC303798
0.8833	High Similarity	NPC286851
0.8667	High Similarity	NPC198341
0.8667	High Similarity	NPC75435
0.8667	High Similarity	NPC471780
0.8667	High Similarity	NPC471892
0.8667	High Similarity	NPC142290
0.8667	High Similarity	NPC223386
0.8525	High Similarity	NPC315980
0.8413	Intermediate Similarity	NPC268922
0.8254	Intermediate Similarity	NPC471418
0.8167	Intermediate Similarity	NPC30126
0.8167	Intermediate Similarity	NPC474014
0.8167	Intermediate Similarity	NPC57846
0.8154	Intermediate Similarity	NPC476694
0.8154	Intermediate Similarity	NPC476695
0.8154	Intermediate Similarity	NPC476696
0.8136	Intermediate Similarity	NPC170172
0.8103	Intermediate Similarity	NPC311668
0.8103	Intermediate Similarity	NPC65832
0.8103	Intermediate Similarity	NPC10262
0.7895	Intermediate Similarity	NPC272396
0.7879	Intermediate Similarity	NPC255535
0.7879	Intermediate Similarity	NPC299603
0.7879	Intermediate Similarity	NPC137554
0.7879	Intermediate Similarity	NPC28959
0.7879	Intermediate Similarity	NPC285014
0.7869	Intermediate Similarity	NPC62507
0.7869	Intermediate Similarity	NPC8087
0.7778	Intermediate Similarity	NPC474928
0.7619	Intermediate Similarity	NPC163134
0.7619	Intermediate Similarity	NPC471419
0.7385	Intermediate Similarity	NPC473952
0.7385	Intermediate Similarity	NPC116377
0.7385	Intermediate Similarity	NPC101746
0.7385	Intermediate Similarity	NPC77191
0.7385	Intermediate Similarity	NPC69798
0.7258	Intermediate Similarity	NPC471421
0.7258	Intermediate Similarity	NPC233364
0.7231	Intermediate Similarity	NPC233034
0.7206	Intermediate Similarity	NPC475694
0.7206	Intermediate Similarity	NPC473710
0.7164	Intermediate Similarity	NPC107224
0.7123	Intermediate Similarity	NPC98750
0.7101	Intermediate Similarity	NPC306973
0.7027	Intermediate Similarity	NPC70574
0.6935	Remote Similarity	NPC8979
0.6912	Remote Similarity	NPC34291
0.6912	Remote Similarity	NPC126664
0.6885	Remote Similarity	NPC275727
0.6842	Remote Similarity	NPC271772
0.6842	Remote Similarity	NPC36927
0.6761	Remote Similarity	NPC474468
0.6721	Remote Similarity	NPC277072
0.6721	Remote Similarity	NPC178263
0.6712	Remote Similarity	NPC477002
0.6711	Remote Similarity	NPC219340
0.6667	Remote Similarity	NPC26932
0.6579	Remote Similarity	NPC83248
0.6579	Remote Similarity	NPC100204
0.6557	Remote Similarity	NPC123814
0.6528	Remote Similarity	NPC185084
0.6522	Remote Similarity	NPC291650
0.6522	Remote Similarity	NPC322801
0.6522	Remote Similarity	NPC129100
0.65	Remote Similarity	NPC469363
0.6471	Remote Similarity	NPC472609
0.6462	Remote Similarity	NPC268927
0.6462	Remote Similarity	NPC64250
0.6462	Remote Similarity	NPC276928
0.6441	Remote Similarity	NPC121062
0.6441	Remote Similarity	NPC96966
0.6441	Remote Similarity	NPC29222
0.6429	Remote Similarity	NPC171850
0.6418	Remote Similarity	NPC17455
0.6406	Remote Similarity	NPC293551
0.6338	Remote Similarity	NPC475127
0.6338	Remote Similarity	NPC473419
0.6338	Remote Similarity	NPC475715
0.6329	Remote Similarity	NPC165119
0.629	Remote Similarity	NPC474322
0.6286	Remote Similarity	NPC135539
0.6286	Remote Similarity	NPC221764
0.6286	Remote Similarity	NPC196359
0.6286	Remote Similarity	NPC78312
0.6286	Remote Similarity	NPC59221
0.6234	Remote Similarity	NPC150557
0.6232	Remote Similarity	NPC41429
0.6197	Remote Similarity	NPC474469
0.6197	Remote Similarity	NPC254617
0.6197	Remote Similarity	NPC74555
0.6197	Remote Similarity	NPC306763
0.6197	Remote Similarity	NPC266242
0.6143	Remote Similarity	NPC294883
0.6143	Remote Similarity	NPC12514
0.6133	Remote Similarity	NPC473588
0.6133	Remote Similarity	NPC78562
0.6076	Remote Similarity	NPC471420
0.6056	Remote Similarity	NPC184150
0.6056	Remote Similarity	NPC141156
0.6027	Remote Similarity	NPC163538
0.6027	Remote Similarity	NPC115800
0.6026	Remote Similarity	NPC473971
0.6026	Remote Similarity	NPC475363
0.6026	Remote Similarity	NPC473972
0.6024	Remote Similarity	NPC306838
0.6	Remote Similarity	NPC208657
0.6	Remote Similarity	NPC242077
0.5968	Remote Similarity	NPC224624
0.589	Remote Similarity	NPC223893
0.589	Remote Similarity	NPC23721
0.5882	Remote Similarity	NPC319131
0.5849	Remote Similarity	NPC328729
0.5811	Remote Similarity	NPC223174
0.5811	Remote Similarity	NPC327486
0.5811	Remote Similarity	NPC327753
0.5714	Remote Similarity	NPC470993
0.5714	Remote Similarity	NPC470992
0.5714	Remote Similarity	NPC145627
0.5714	Remote Similarity	NPC47333
0.5692	Remote Similarity	NPC270041
0.5658	Remote Similarity	NPC55274
0.5652	Remote Similarity	NPC68974
0.5641	Remote Similarity	NPC244539
0.5634	Remote Similarity	NPC106216
0.5634	Remote Similarity	NPC88898
0.5614	Remote Similarity	NPC167301
0.5606	Remote Similarity	NPC471423
0.5606	Remote Similarity	NPC471442

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 NPC204709 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	70
0.1-0.2	3565
0.2-0.3	4164
0.3-0.4	955
0.4-0.5	299
0.5-0.6	70
0.6-0.7	17
0.7-0.8	5
0.8-0.85	1
0.85-0.9	4
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8966	High Similarity	NPD9027	Phase 3
0.8966	High Similarity	NPD9026	Phase 2
0.8966	High Similarity	NPD9028	Phase 2
0.8966	High Similarity	NPD9029	Phase 3
0.8167	Intermediate Similarity	NPD9024	Phase 2
0.8167	Intermediate Similarity	NPD9022	Phase 2
0.7869	Intermediate Similarity	NPD393	Approved
0.7705	Intermediate Similarity	NPD9239	Approved
0.7705	Intermediate Similarity	NPD9240	Approved
0.7705	Intermediate Similarity	NPD9455	Approved
0.7231	Intermediate Similarity	NPD9440	Discontinued
0.6912	Remote Similarity	NPD9443	Clinical (unspecified phase)
0.6582	Remote Similarity	NPD9401	Discovery
0.6557	Remote Similarity	NPD3215	Phase 1
0.6552	Remote Similarity	NPD398	Approved
0.6552	Remote Similarity	NPD399	Approved
0.6552	Remote Similarity	NPD400	Approved
0.6522	Remote Similarity	NPD9031	Approved
0.6522	Remote Similarity	NPD9030	Approved
0.6522	Remote Similarity	NPD9033	Approved
0.6522	Remote Similarity	NPD9032	Approved
0.6377	Remote Similarity	NPD9442	Clinical (unspecified phase)
0.6286	Remote Similarity	NPD8868	Approved
0.623	Remote Similarity	NPD3214	Discontinued
0.6098	Remote Similarity	NPD394	Phase 3
0.6	Remote Similarity	NPD9646	Approved
0.6	Remote Similarity	NPD9644	Approved
0.6	Remote Similarity	NPD9034	Approved
0.6	Remote Similarity	NPD9645	Approved
0.6	Remote Similarity	NPD67	Phase 2
0.5972	Remote Similarity	NPD9444	Discontinued
0.5926	Remote Similarity	NPD883	Phase 2
0.5926	Remote Similarity	NPD882	Phase 2
0.5857	Remote Similarity	NPD9211	Clinical (unspecified phase)
0.5849	Remote Similarity	NPD8556	Phase 3
0.5811	Remote Similarity	NPD9445	Approved
0.5783	Remote Similarity	NPD9654	Phase 2
0.5781	Remote Similarity	NPD9668	Phase 2
0.5775	Remote Similarity	NPD9648	Approved
0.569	Remote Similarity	NPD9227	Discontinued
0.5658	Remote Similarity	NPD6704	Discontinued

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