Structure

Physi-Chem Properties

Molecular Weight:  177.1
Volume:  167.23
LogP:  -1.571
LogD:  -1.824
LogS:  -0.161
# Rotatable Bonds:  1
TPSA:  92.95
# H-Bond Aceptor:  5
# H-Bond Donor:  5
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.303
Synthetic Accessibility Score:  4.141
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:  -5.354
MDCK Permeability:  0.00022642838302999735
Pgp-inhibitor:  0.0
Pgp-substrate:  0.732
Human Intestinal Absorption (HIA):  0.893
20% Bioavailability (F20%):  0.03
30% Bioavailability (F30%):  0.908

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.226
Plasma Protein Binding (PPB):  14.903261184692383%
Volume Distribution (VD):  0.457
Pgp-substrate:  85.66484832763672%

ADMET: Metabolism

CYP1A2-inhibitor:  0.023
CYP1A2-substrate:  0.048
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.483
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.142
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.194
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.02

ADMET: Excretion

Clearance (CL):  2.505
Half-life (T1/2):  0.684

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.936
Drug-inuced Liver Injury (DILI):  0.287
AMES Toxicity:  0.031
Rat Oral Acute Toxicity:  0.008
Maximum Recommended Daily Dose:  0.049
Skin Sensitization:  0.324
Carcinogencity:  0.013
Eye Corrosion:  0.01
Eye Irritation:  0.138
Respiratory Toxicity:  0.602

Download Data

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

  Natural Product: NPC303798

Natural Product ID:  NPC303798
Common Name*:   Beta-Homofuconojirimycin
IUPAC Name:   (2R,3R,4R,5R,6S)-2-(hydroxymethyl)-6-methylpiperidine-3,4,5-triol
Synonyms:   Beta-Homofuconojirimycin
Standard InCHIKey:  ZEWFPWKROPWRKE-CQOGJGKDSA-N
Standard InCHI:  InChI=1S/C7H15NO4/c1-3-5(10)7(12)6(11)4(2-9)8-3/h3-12H,2H2,1H3/t3-,4+,5+,6+,7+/m0/s1
SMILES:  C[C@H]1[C@H]([C@H]([C@@H]([C@@H](CO)N1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL87474
PubChem CID:   469851
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
NPO25301 Angylocalyx pynaertii Species Fabaceae Eukaryota pods n.a. n.a. PMID[11858756]
NPO25301 Angylocalyx pynaertii Species Fabaceae Eukaryota seeds n.a. n.a. PMID[8229017]
NPO25301 Angylocalyx pynaertii Species Fabaceae 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

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[473643]
NPT496 Individual Protein Alpha-L-fucosidase 1 Bos taurus Ki = 5.3 nM PMID[473644]
NPT496 Individual Protein Alpha-L-fucosidase 1 Bos taurus Ki = 5.3 nM PMID[473645]

☑ 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 NPC303798 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC286851
0.9833 High Similarity NPC198341
0.9833 High Similarity NPC471892
0.9833 High Similarity NPC75435
0.9833 High Similarity NPC471780
0.9833 High Similarity NPC223386
0.9833 High Similarity NPC142290
0.9524 High Similarity NPC268922
0.95 High Similarity NPC2432
0.95 High Similarity NPC69669
0.95 High Similarity NPC150680
0.95 High Similarity NPC218150
0.95 High Similarity NPC306462
0.95 High Similarity NPC22774
0.9365 High Similarity NPC471418
0.9231 High Similarity NPC476694
0.9231 High Similarity NPC476696
0.9231 High Similarity NPC476695
0.9048 High Similarity NPC315980
0.9 High Similarity NPC290106
0.9 High Similarity NPC193593
0.9 High Similarity NPC76726
0.9 High Similarity NPC143809
0.8939 High Similarity NPC137554
0.8939 High Similarity NPC255535
0.8939 High Similarity NPC299603
0.8939 High Similarity NPC285014
0.8939 High Similarity NPC28959
0.8833 High Similarity NPC204709
0.873 High Similarity NPC471419
0.873 High Similarity NPC163134
0.8689 High Similarity NPC170172
0.8462 Intermediate Similarity NPC101746
0.8462 Intermediate Similarity NPC116377
0.8462 Intermediate Similarity NPC473952
0.8462 Intermediate Similarity NPC77191
0.8462 Intermediate Similarity NPC69798
0.8308 Intermediate Similarity NPC474928
0.8235 Intermediate Similarity NPC473710
0.8235 Intermediate Similarity NPC475694
0.8095 Intermediate Similarity NPC471421
0.8095 Intermediate Similarity NPC233364
0.7941 Intermediate Similarity NPC126664
0.7941 Intermediate Similarity NPC34291
0.7846 Intermediate Similarity NPC8087
0.7846 Intermediate Similarity NPC30126
0.7846 Intermediate Similarity NPC57846
0.7846 Intermediate Similarity NPC62507
0.7846 Intermediate Similarity NPC474014
0.7763 Intermediate Similarity NPC271772
0.7763 Intermediate Similarity NPC36927
0.7746 Intermediate Similarity NPC474468
0.76 Intermediate Similarity NPC98750
0.75 Intermediate Similarity NPC311668
0.75 Intermediate Similarity NPC70574
0.75 Intermediate Similarity NPC10262
0.75 Intermediate Similarity NPC65832
0.75 Intermediate Similarity NPC233034
0.7231 Intermediate Similarity NPC8979
0.7215 Intermediate Similarity NPC165119
0.7183 Intermediate Similarity NPC171850
0.7179 Intermediate Similarity NPC219340
0.7143 Intermediate Similarity NPC150557
0.7123 Intermediate Similarity NPC306973
0.7051 Intermediate Similarity NPC83248
0.7051 Intermediate Similarity NPC100204
0.7042 Intermediate Similarity NPC322801
0.7042 Intermediate Similarity NPC129100
0.7042 Intermediate Similarity NPC291650
0.7031 Intermediate Similarity NPC272396
0.6986 Remote Similarity NPC163538
0.6986 Remote Similarity NPC115800
0.6962 Remote Similarity NPC471420
0.6951 Remote Similarity NPC469363
0.6944 Remote Similarity NPC107224
0.6867 Remote Similarity NPC306838
0.6849 Remote Similarity NPC473419
0.6849 Remote Similarity NPC475715
0.6849 Remote Similarity NPC475127
0.6769 Remote Similarity NPC178263
0.6769 Remote Similarity NPC277072
0.6753 Remote Similarity NPC477002
0.6712 Remote Similarity NPC266242
0.6712 Remote Similarity NPC306763
0.6712 Remote Similarity NPC474469
0.6712 Remote Similarity NPC74555
0.6712 Remote Similarity NPC254617
0.6667 Remote Similarity NPC12514
0.6667 Remote Similarity NPC294883
0.6667 Remote Similarity NPC275727
0.6615 Remote Similarity NPC123814
0.6579 Remote Similarity NPC185084
0.6575 Remote Similarity NPC59221
0.6575 Remote Similarity NPC184150
0.6575 Remote Similarity NPC141156
0.6538 Remote Similarity NPC244539
0.6508 Remote Similarity NPC29222
0.6508 Remote Similarity NPC96966
0.6508 Remote Similarity NPC121062
0.6479 Remote Similarity NPC17455
0.6456 Remote Similarity NPC313762
0.6364 Remote Similarity NPC474322
0.6316 Remote Similarity NPC327753
0.6316 Remote Similarity NPC327486
0.6316 Remote Similarity NPC223174
0.6301 Remote Similarity NPC472609
0.6282 Remote Similarity NPC26932
0.625 Remote Similarity NPC145627
0.6237 Remote Similarity NPC315170
0.622 Remote Similarity NPC314762
0.6197 Remote Similarity NPC319131
0.617 Remote Similarity NPC56298
0.617 Remote Similarity NPC471628
0.617 Remote Similarity NPC315036
0.6098 Remote Similarity NPC473972
0.6098 Remote Similarity NPC473971
0.6098 Remote Similarity NPC475363
0.6076 Remote Similarity NPC208657
0.6056 Remote Similarity NPC276928
0.6056 Remote Similarity NPC64250
0.6056 Remote Similarity NPC268927
0.6024 Remote Similarity NPC318258
0.6023 Remote Similarity NPC470282
0.5976 Remote Similarity NPC314968
0.5976 Remote Similarity NPC314772
0.5949 Remote Similarity NPC55274
0.5921 Remote Similarity NPC135539
0.5921 Remote Similarity NPC196359
0.5921 Remote Similarity NPC78312
0.5921 Remote Similarity NPC221764
0.5882 Remote Similarity NPC315969
0.5862 Remote Similarity NPC125253
0.5862 Remote Similarity NPC192025
0.5862 Remote Similarity NPC253975
0.5844 Remote Similarity NPC195165
0.5814 Remote Similarity NPC263058
0.5811 Remote Similarity NPC47333
0.5797 Remote Similarity NPC270041
0.5795 Remote Similarity NPC83839
0.5775 Remote Similarity NPC293551
0.5769 Remote Similarity NPC223893
0.5753 Remote Similarity NPC68974
0.5733 Remote Similarity NPC106216
0.5733 Remote Similarity NPC88898
0.5732 Remote Similarity NPC140327
0.5732 Remote Similarity NPC62293
0.5732 Remote Similarity NPC212008
0.5732 Remote Similarity NPC51055
0.5714 Remote Similarity NPC471442
0.5714 Remote Similarity NPC471423
0.5714 Remote Similarity NPC316807
0.5694 Remote Similarity NPC168308
0.5694 Remote Similarity NPC302569
0.5684 Remote Similarity NPC313821
0.5673 Remote Similarity NPC314306
0.5658 Remote Similarity NPC41429
0.5657 Remote Similarity NPC221148
0.5644 Remote Similarity NPC313272
0.5644 Remote Similarity NPC319537
0.5625 Remote Similarity NPC477200
0.5616 Remote Similarity NPC216415
0.5616 Remote Similarity NPC319991
0.5616 Remote Similarity NPC476537
0.561 Remote Similarity NPC473588
0.561 Remote Similarity NPC78562

  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 NPC303798 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.95 High Similarity NPD9028 Phase 2
0.95 High Similarity NPD9029 Phase 3
0.95 High Similarity NPD9026 Phase 2
0.95 High Similarity NPD9027 Phase 3
0.8413 Intermediate Similarity NPD393 Approved
0.8254 Intermediate Similarity NPD9240 Approved
0.8254 Intermediate Similarity NPD9239 Approved
0.8254 Intermediate Similarity NPD9455 Approved
0.7941 Intermediate Similarity NPD9443 Clinical (unspecified phase)
0.7576 Intermediate Similarity NPD9022 Phase 2
0.7576 Intermediate Similarity NPD9024 Phase 2
0.75 Intermediate Similarity NPD9440 Discontinued
0.7042 Intermediate Similarity NPD9031 Approved
0.7042 Intermediate Similarity NPD9033 Approved
0.7042 Intermediate Similarity NPD9032 Approved
0.7042 Intermediate Similarity NPD9030 Approved
0.7037 Intermediate Similarity NPD9401 Discovery
0.6951 Remote Similarity NPD394 Phase 3
0.6944 Remote Similarity NPD9444 Discontinued
0.679 Remote Similarity NPD882 Phase 2
0.679 Remote Similarity NPD883 Phase 2
0.6615 Remote Similarity NPD3215 Phase 1
0.6494 Remote Similarity NPD67 Phase 2
0.6494 Remote Similarity NPD9034 Approved
0.6316 Remote Similarity NPD9445 Approved
0.6308 Remote Similarity NPD3214 Discontinued
0.617 Remote Similarity NPD4837 Approved
0.617 Remote Similarity NPD4838 Approved
0.617 Remote Similarity NPD4836 Approved
0.617 Remote Similarity NPD4835 Approved
0.6154 Remote Similarity NPD6704 Discontinued
0.6049 Remote Similarity NPD372 Clinical (unspecified phase)
0.5976 Remote Similarity NPD9434 Approved
0.5976 Remote Similarity NPD9435 Approved
0.5957 Remote Similarity NPD4282 Approved
0.5921 Remote Similarity NPD8868 Approved
0.5918 Remote Similarity NPD2700 Approved
0.5846 Remote Similarity NPD398 Approved
0.5846 Remote Similarity NPD400 Approved
0.5846 Remote Similarity NPD399 Approved
0.5816 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5789 Remote Similarity NPD9442 Clinical (unspecified phase)
0.5733 Remote Similarity NPD9211 Clinical (unspecified phase)
0.5684 Remote Similarity NPD3190 Approved
0.5684 Remote Similarity NPD3189 Approved
0.5684 Remote Similarity NPD3191 Approved
0.5673 Remote Similarity NPD6430 Approved
0.5673 Remote Similarity NPD6429 Approved
0.5657 Remote Similarity NPD1449 Approved
0.5657 Remote Similarity NPD1450 Approved
0.5647 Remote Similarity NPD9429 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