Structure

Physi-Chem Properties

Molecular Weight:  147.09
Volume:  141.143
LogP:  -1.854
LogD:  -1.851
LogS:  0.231
# Rotatable Bonds:  1
TPSA:  72.72
# H-Bond Aceptor:  4
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.348
Synthetic Accessibility Score:  3.898
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:  -5.124
MDCK Permeability:  0.000832577992696315
Pgp-inhibitor:  0.0
Pgp-substrate:  0.507
Human Intestinal Absorption (HIA):  0.807
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.09

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.162
Plasma Protein Binding (PPB):  12.417351722717285%
Volume Distribution (VD):  0.62
Pgp-substrate:  89.21661376953125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.014
CYP1A2-substrate:  0.083
CYP2C19-inhibitor:  0.017
CYP2C19-substrate:  0.638
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.159
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.22
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.038

ADMET: Excretion

Clearance (CL):  4.506
Half-life (T1/2):  0.641

ADMET: Toxicity

hERG Blockers:  0.031
Human Hepatotoxicity (H-HT):  0.293
Drug-inuced Liver Injury (DILI):  0.034
AMES Toxicity:  0.045
Rat Oral Acute Toxicity:  0.022
Maximum Recommended Daily Dose:  0.025
Skin Sensitization:  0.629
Carcinogencity:  0.153
Eye Corrosion:  0.166
Eye Irritation:  0.624
Respiratory Toxicity:  0.596

Download Data

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

  Natural Product: NPC143809

Natural Product ID:  NPC143809
Common Name*:   (2S,3S,4R)-2-Hydroxymethylpiperidine-3,4-Diol
IUPAC Name:   (2S,3S,4R)-2-(hydroxymethyl)piperidine-3,4-diol
Synonyms:  
Standard InCHIKey:  YZNNBIPIQWYLDM-JKUQZMGJSA-N
Standard InCHI:  InChI=1S/C6H13NO3/c8-3-4-6(10)5(9)1-2-7-4/h4-10H,1-3H2/t4-,5+,6-/m0/s1
SMILES:  OC[C@@H]1NCC[C@H]([C@H]1O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1818436
PubChem CID:   11389465
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
NPO9402 Morus mongolica Species Moraceae Eukaryota n.a. n.a. n.a. PMID[11429996]
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 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]
NPO28265 Morus alba Species Moraceae Eukaryota Root barks n.a. n.a. PMID[3097265]
NPO9402 Morus mongolica Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
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]
NPO9402 Morus mongolica 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]
NPO9402 Morus mongolica 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]
NPO9402 Morus mongolica Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1051 Individual Protein Lactase-glycosylceramidase Rattus norvegicus IC50 = 122000.0 nM PMID[506340]
NPT462 Individual Protein Sucrase-isomaltase Rattus norvegicus IC50 = 225000.0 nM PMID[506340]
NPT462 Individual Protein Sucrase-isomaltase Rattus norvegicus Inhibition < 50.0 % PMID[506340]
NPT3767 Individual Protein Glucosylceramidase Bos taurus Inhibition < 50.0 % PMID[506340]
NPT61 Individual Protein Beta-glucocerebrosidase Homo sapiens Inhibition < 50.0 % PMID[506340]
NPT509 Individual Protein Beta-galactosidase Bos taurus IC50 = 960000.0 nM PMID[506340]
NPT496 Individual Protein Alpha-L-fucosidase 1 Bos taurus IC50 = 260000.0 nM PMID[506340]
NPT3907 Individual Protein Ceramide glucosyltransferase Mus musculus IC50 > 10000.0 nM PMID[506341]
NPT513 Individual Protein Beta-glucosidase Homo sapiens IC50 = 30000.0 nM PMID[506341]
NPT2 Others Unspecified Inhibition < 50.0 % PMID[506340]
NPT2 Others Unspecified IC50 = 357000.0 nM PMID[506340]
NPT2 Others Unspecified IC50 = 809000.0 nM PMID[506340]
NPT2 Others Unspecified IC50 = 188000.0 nM PMID[506340]
NPT2 Others Unspecified IC50 > 1000000.0 nM PMID[506341]

☑ 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 NPC143809 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 NPC76726
1.0 High Similarity NPC290106
1.0 High Similarity NPC193593
0.9474 High Similarity NPC69669
0.9474 High Similarity NPC2432
0.9474 High Similarity NPC22774
0.9474 High Similarity NPC150680
0.9474 High Similarity NPC218150
0.9474 High Similarity NPC306462
0.9455 High Similarity NPC204709
0.9153 High Similarity NPC223386
0.9153 High Similarity NPC75435
0.9153 High Similarity NPC471892
0.9153 High Similarity NPC198341
0.9153 High Similarity NPC471780
0.9153 High Similarity NPC142290
0.9 High Similarity NPC315980
0.9 High Similarity NPC303798
0.9 High Similarity NPC286851
0.871 High Similarity NPC471418
0.8571 High Similarity NPC268922
0.8333 Intermediate Similarity NPC8087
0.8333 Intermediate Similarity NPC30126
0.8333 Intermediate Similarity NPC474014
0.8333 Intermediate Similarity NPC57846
0.8333 Intermediate Similarity NPC62507
0.8308 Intermediate Similarity NPC299603
0.8308 Intermediate Similarity NPC28959
0.8308 Intermediate Similarity NPC255535
0.8308 Intermediate Similarity NPC137554
0.8308 Intermediate Similarity NPC476696
0.8308 Intermediate Similarity NPC285014
0.8308 Intermediate Similarity NPC476694
0.8308 Intermediate Similarity NPC476695
0.8305 Intermediate Similarity NPC170172
0.8276 Intermediate Similarity NPC65832
0.8276 Intermediate Similarity NPC311668
0.8276 Intermediate Similarity NPC10262
0.7937 Intermediate Similarity NPC474928
0.7812 Intermediate Similarity NPC116377
0.7812 Intermediate Similarity NPC77191
0.7812 Intermediate Similarity NPC101746
0.7812 Intermediate Similarity NPC69798
0.7812 Intermediate Similarity NPC473952
0.7778 Intermediate Similarity NPC471419
0.7778 Intermediate Similarity NPC163134
0.7759 Intermediate Similarity NPC272396
0.7656 Intermediate Similarity NPC233034
0.7576 Intermediate Similarity NPC107224
0.75 Intermediate Similarity NPC98750
0.7397 Intermediate Similarity NPC70574
0.7353 Intermediate Similarity NPC475694
0.7353 Intermediate Similarity NPC473710
0.7313 Intermediate Similarity NPC34291
0.7313 Intermediate Similarity NPC126664
0.72 Intermediate Similarity NPC271772
0.72 Intermediate Similarity NPC36927
0.7143 Intermediate Similarity NPC474468
0.7143 Intermediate Similarity NPC471421
0.7143 Intermediate Similarity NPC233364
0.7097 Intermediate Similarity NPC8979
0.7067 Intermediate Similarity NPC219340
0.7049 Intermediate Similarity NPC275727
0.7 Intermediate Similarity NPC306973
0.6933 Remote Similarity NPC100204
0.6933 Remote Similarity NPC83248
0.6912 Remote Similarity NPC291650
0.6912 Remote Similarity NPC129100
0.6912 Remote Similarity NPC322801
0.6901 Remote Similarity NPC185084
0.6835 Remote Similarity NPC469363
0.6667 Remote Similarity NPC165119
0.6622 Remote Similarity NPC477002
0.6618 Remote Similarity NPC472609
0.6615 Remote Similarity NPC268927
0.6615 Remote Similarity NPC276928
0.6615 Remote Similarity NPC64250
0.6613 Remote Similarity NPC277072
0.6613 Remote Similarity NPC178263
0.6571 Remote Similarity NPC171850
0.6571 Remote Similarity NPC474469
0.6522 Remote Similarity NPC294883
0.6522 Remote Similarity NPC12514
0.6479 Remote Similarity NPC473419
0.6479 Remote Similarity NPC475715
0.6479 Remote Similarity NPC475127
0.6452 Remote Similarity NPC123814
0.6429 Remote Similarity NPC59221
0.6429 Remote Similarity NPC196359
0.6429 Remote Similarity NPC78312
0.6429 Remote Similarity NPC135539
0.6429 Remote Similarity NPC221764
0.6429 Remote Similarity NPC141156
0.6429 Remote Similarity NPC184150
0.6364 Remote Similarity NPC150557
0.6351 Remote Similarity NPC26932
0.6341 Remote Similarity NPC306838
0.6338 Remote Similarity NPC254617
0.6338 Remote Similarity NPC306763
0.6338 Remote Similarity NPC266242
0.6338 Remote Similarity NPC74555
0.6333 Remote Similarity NPC121062
0.6333 Remote Similarity NPC29222
0.6333 Remote Similarity NPC96966
0.6324 Remote Similarity NPC17455
0.6203 Remote Similarity NPC471420
0.619 Remote Similarity NPC474322
0.6164 Remote Similarity NPC163538
0.6164 Remote Similarity NPC115800
0.6061 Remote Similarity NPC293551
0.5974 Remote Similarity NPC244539
0.5949 Remote Similarity NPC475363
0.5949 Remote Similarity NPC473971
0.5949 Remote Similarity NPC473972
0.5946 Remote Similarity NPC327486
0.5946 Remote Similarity NPC223174
0.5946 Remote Similarity NPC327753
0.5921 Remote Similarity NPC208657
0.5915 Remote Similarity NPC41429
0.5897 Remote Similarity NPC313762
0.5875 Remote Similarity NPC318258
0.5873 Remote Similarity NPC224624
0.5857 Remote Similarity NPC145627
0.5844 Remote Similarity NPC78562
0.5844 Remote Similarity NPC473588
0.5811 Remote Similarity NPC223893
0.5797 Remote Similarity NPC319131
0.5797 Remote Similarity NPC68974
0.5775 Remote Similarity NPC88898
0.5775 Remote Similarity NPC106216
0.5761 Remote Similarity NPC315170
0.5741 Remote Similarity NPC328729
0.5732 Remote Similarity NPC242077
0.5732 Remote Similarity NPC315969
0.5679 Remote Similarity NPC314762
0.5663 Remote Similarity NPC263058
0.5634 Remote Similarity NPC47333
0.5625 Remote Similarity NPC314772
0.5625 Remote Similarity NPC314968
0.5606 Remote Similarity NPC270041
0.56 Remote Similarity NPC23721

  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 NPC143809 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
0.9474 High Similarity NPD9029 Phase 3
0.9474 High Similarity NPD9028 Phase 2
0.9474 High Similarity NPD9026 Phase 2
0.9474 High Similarity NPD9027 Phase 3
0.8333 Intermediate Similarity NPD9022 Phase 2
0.8333 Intermediate Similarity NPD9024 Phase 2
0.8167 Intermediate Similarity NPD9455 Approved
0.8033 Intermediate Similarity NPD393 Approved
0.7869 Intermediate Similarity NPD9239 Approved
0.7869 Intermediate Similarity NPD9240 Approved
0.7656 Intermediate Similarity NPD9440 Discontinued
0.7313 Intermediate Similarity NPD9443 Clinical (unspecified phase)
0.6923 Remote Similarity NPD9401 Discovery
0.6912 Remote Similarity NPD9031 Approved
0.6912 Remote Similarity NPD9030 Approved
0.6912 Remote Similarity NPD9032 Approved
0.6912 Remote Similarity NPD9033 Approved
0.6452 Remote Similarity NPD3215 Phase 1
0.6429 Remote Similarity NPD8868 Approved
0.642 Remote Similarity NPD394 Phase 3
0.6351 Remote Similarity NPD9034 Approved
0.6351 Remote Similarity NPD67 Phase 2
0.6338 Remote Similarity NPD9444 Discontinued
0.6167 Remote Similarity NPD400 Approved
0.6167 Remote Similarity NPD399 Approved
0.6167 Remote Similarity NPD398 Approved
0.6129 Remote Similarity NPD3214 Discontinued
0.6056 Remote Similarity NPD9442 Clinical (unspecified phase)
0.6049 Remote Similarity NPD882 Phase 2
0.6049 Remote Similarity NPD883 Phase 2
0.5946 Remote Similarity NPD9445 Approved
0.5897 Remote Similarity NPD372 Clinical (unspecified phase)
0.5789 Remote Similarity NPD6704 Discontinued
0.5775 Remote Similarity NPD9211 Clinical (unspecified phase)
0.5741 Remote Similarity NPD8556 Phase 3
0.5732 Remote Similarity NPD9646 Approved
0.5732 Remote Similarity NPD9644 Approved
0.5732 Remote Similarity NPD9645 Approved
0.5679 Remote Similarity NPD9429 Discontinued
0.5652 Remote Similarity NPD4282 Approved
0.5625 Remote Similarity NPD9434 Approved
0.5625 Remote Similarity NPD9435 Approved

  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