Structure

Physi-Chem Properties

Molecular Weight:  222.11
Volume:  208.405
LogP:  -1.059
LogD:  -1.442
LogS:  -0.056
# Rotatable Bonds:  3
TPSA:  99.38
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.45
Synthetic Accessibility Score:  3.627
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.308
MDCK Permeability:  0.00032206365722231567
Pgp-inhibitor:  0.001
Pgp-substrate:  0.034
Human Intestinal Absorption (HIA):  0.088
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.15

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.274
Plasma Protein Binding (PPB):  16.056110382080078%
Volume Distribution (VD):  0.654
Pgp-substrate:  72.56212615966797%

ADMET: Metabolism

CYP1A2-inhibitor:  0.026
CYP1A2-substrate:  0.071
CYP2C19-inhibitor:  0.018
CYP2C19-substrate:  0.681
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.08
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.144
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.077

ADMET: Excretion

Clearance (CL):  2.212
Half-life (T1/2):  0.82

ADMET: Toxicity

hERG Blockers:  0.036
Human Hepatotoxicity (H-HT):  0.163
Drug-inuced Liver Injury (DILI):  0.079
AMES Toxicity:  0.443
Rat Oral Acute Toxicity:  0.029
Maximum Recommended Daily Dose:  0.004
Skin Sensitization:  0.078
Carcinogencity:  0.046
Eye Corrosion:  0.009
Eye Irritation:  0.76
Respiratory Toxicity:  0.019

Download Data

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

  Natural Product: NPC23134

Natural Product ID:  NPC23134
Common Name*:   Isopropyl O-Beta-D-Glucopyranoside
IUPAC Name:   (2R,3S,4S,5R,6R)-2-(hydroxymethyl)-6-propan-2-yloxyoxane-3,4,5-triol
Synonyms:  
Standard InCHIKey:  UOEFDXYUEPHESS-SYHAXYEDSA-N
Standard InCHI:  InChI=1S/C9H18O6/c1-4(2)14-9-8(13)7(12)6(11)5(3-10)15-9/h4-13H,3H2,1-2H3/t5-,6-,7+,8-,9-/m1/s1
SMILES:  OC[C@H]1O[C@@H](OC(C)C)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3326714
PubChem CID:   21572943
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002207] O-glycosyl compounds

*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
NPO30686 Citrus hystrix Species Rutaceae Eukaryota n.a. exocarp n.a. PMID[20964319]
NPO6648 Piper retrofractum Species Piperaceae Eukaryota Fruits n.a. n.a. PMID[23506561]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[24813739]
NPO6648 Piper retrofractum Species Piperaceae Eukaryota leaves n.a. n.a. PMID[25127165]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6648 Piper retrofractum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6648 Piper retrofractum Species Piperaceae 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
NPT60 Individual Protein Lysosomal alpha-glucosidase Homo sapiens Inhibition = 7.31 % PMID[552021]
NPT35 Others n.a. Activity = 0.22 uM PMID[552021]
NPT35 Others n.a. Activity = 1.79 uM PMID[552021]
NPT35 Others n.a. Activity = 0.29 uM PMID[552021]
NPT35 Others n.a. Activity = 0.54 uM PMID[552021]
NPT35 Others n.a. Activity = 20.97 % PMID[552021]

☑ 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 NPC23134 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 NPC233726
1.0 High Similarity NPC124963
0.9583 High Similarity NPC326533
0.9574 High Similarity NPC157193
0.9574 High Similarity NPC282143
0.9574 High Similarity NPC299781
0.9574 High Similarity NPC42503
0.94 High Similarity NPC303727
0.9362 High Similarity NPC14144
0.92 High Similarity NPC157514
0.92 High Similarity NPC89145
0.92 High Similarity NPC242073
0.92 High Similarity NPC323361
0.92 High Similarity NPC58629
0.92 High Similarity NPC145112
0.92 High Similarity NPC246558
0.92 High Similarity NPC269166
0.92 High Similarity NPC165198
0.92 High Similarity NPC107914
0.92 High Similarity NPC130683
0.92 High Similarity NPC67660
0.9149 High Similarity NPC277475
0.9149 High Similarity NPC321087
0.9038 High Similarity NPC148424
0.898 High Similarity NPC323574
0.8936 High Similarity NPC165846
0.8936 High Similarity NPC255377
0.8936 High Similarity NPC69445
0.8936 High Similarity NPC199857
0.8936 High Similarity NPC21209
0.8936 High Similarity NPC73906
0.8936 High Similarity NPC92246
0.8936 High Similarity NPC285364
0.8936 High Similarity NPC176017
0.8936 High Similarity NPC289758
0.8868 High Similarity NPC219040
0.8868 High Similarity NPC472025
0.8776 High Similarity NPC82512
0.8704 High Similarity NPC320032
0.8704 High Similarity NPC322855
0.8545 High Similarity NPC143326
0.8511 High Similarity NPC70756
0.8511 High Similarity NPC320240
0.8393 Intermediate Similarity NPC477757
0.8393 Intermediate Similarity NPC155457
0.8393 Intermediate Similarity NPC477762
0.8393 Intermediate Similarity NPC472026
0.8393 Intermediate Similarity NPC477763
0.8393 Intermediate Similarity NPC477750
0.8393 Intermediate Similarity NPC477755
0.8393 Intermediate Similarity NPC477753
0.8367 Intermediate Similarity NPC230789
0.8367 Intermediate Similarity NPC252918
0.8364 Intermediate Similarity NPC290179
0.8364 Intermediate Similarity NPC34877
0.8364 Intermediate Similarity NPC317023
0.8298 Intermediate Similarity NPC298699
0.8298 Intermediate Similarity NPC291502
0.8298 Intermediate Similarity NPC86191
0.8298 Intermediate Similarity NPC134252
0.8298 Intermediate Similarity NPC213159
0.8298 Intermediate Similarity NPC317182
0.8103 Intermediate Similarity NPC277570
0.8103 Intermediate Similarity NPC325773
0.7966 Intermediate Similarity NPC294813
0.7966 Intermediate Similarity NPC31496
0.7966 Intermediate Similarity NPC13143
0.7872 Intermediate Similarity NPC266553
0.7833 Intermediate Similarity NPC190418
0.7833 Intermediate Similarity NPC471761
0.7833 Intermediate Similarity NPC76881
0.7833 Intermediate Similarity NPC471760
0.7833 Intermediate Similarity NPC12040
0.7833 Intermediate Similarity NPC147292
0.7797 Intermediate Similarity NPC268243
0.7778 Intermediate Similarity NPC317626
0.7778 Intermediate Similarity NPC314821
0.7778 Intermediate Similarity NPC317501
0.7755 Intermediate Similarity NPC29721
0.7705 Intermediate Similarity NPC477764
0.7705 Intermediate Similarity NPC477756
0.7705 Intermediate Similarity NPC477751
0.7705 Intermediate Similarity NPC477752
0.7667 Intermediate Similarity NPC6848
0.7581 Intermediate Similarity NPC477760
0.7581 Intermediate Similarity NPC477759
0.7581 Intermediate Similarity NPC477754
0.7581 Intermediate Similarity NPC477758
0.7581 Intermediate Similarity NPC206601
0.7581 Intermediate Similarity NPC477761
0.7551 Intermediate Similarity NPC320189
0.746 Intermediate Similarity NPC50228
0.746 Intermediate Similarity NPC97736
0.746 Intermediate Similarity NPC250619
0.746 Intermediate Similarity NPC67099
0.7344 Intermediate Similarity NPC211428
0.7344 Intermediate Similarity NPC285003
0.7344 Intermediate Similarity NPC241265
0.7302 Intermediate Similarity NPC32148
0.7255 Intermediate Similarity NPC107091
0.7255 Intermediate Similarity NPC207656
0.7231 Intermediate Similarity NPC53760
0.7231 Intermediate Similarity NPC52268
0.7231 Intermediate Similarity NPC474078
0.7121 Intermediate Similarity NPC185419
0.7121 Intermediate Similarity NPC184550
0.7015 Intermediate Similarity NPC291228
0.7015 Intermediate Similarity NPC163812
0.7015 Intermediate Similarity NPC169085
0.7015 Intermediate Similarity NPC206823
0.7015 Intermediate Similarity NPC225748
0.7015 Intermediate Similarity NPC308096
0.7015 Intermediate Similarity NPC9763
0.7015 Intermediate Similarity NPC39266
0.6981 Remote Similarity NPC88638
0.697 Remote Similarity NPC471879
0.6912 Remote Similarity NPC166250
0.6912 Remote Similarity NPC472173
0.6912 Remote Similarity NPC308489
0.6912 Remote Similarity NPC472174
0.6897 Remote Similarity NPC326557
0.6809 Remote Similarity NPC293908
0.6809 Remote Similarity NPC86412
0.6809 Remote Similarity NPC325034
0.6809 Remote Similarity NPC66052
0.6809 Remote Similarity NPC192065
0.6786 Remote Similarity NPC329095
0.6769 Remote Similarity NPC179823
0.6765 Remote Similarity NPC470659
0.6765 Remote Similarity NPC55652
0.6765 Remote Similarity NPC132938
0.6765 Remote Similarity NPC470660
0.6714 Remote Similarity NPC326661
0.6714 Remote Similarity NPC477350
0.6714 Remote Similarity NPC229655
0.6714 Remote Similarity NPC279575
0.6667 Remote Similarity NPC258690
0.6667 Remote Similarity NPC320043
0.6667 Remote Similarity NPC103672
0.6667 Remote Similarity NPC317651
0.662 Remote Similarity NPC476783
0.662 Remote Similarity NPC110813
0.662 Remote Similarity NPC476782
0.662 Remote Similarity NPC188793
0.662 Remote Similarity NPC216883
0.662 Remote Similarity NPC476781
0.6607 Remote Similarity NPC322158
0.6607 Remote Similarity NPC329128
0.6567 Remote Similarity NPC327753
0.6567 Remote Similarity NPC223174
0.6567 Remote Similarity NPC327486
0.6528 Remote Similarity NPC477325
0.6528 Remote Similarity NPC475425
0.6528 Remote Similarity NPC113745
0.6528 Remote Similarity NPC477330
0.6528 Remote Similarity NPC177343
0.6528 Remote Similarity NPC477328
0.6528 Remote Similarity NPC133377
0.6528 Remote Similarity NPC477329
0.6528 Remote Similarity NPC109887
0.6528 Remote Similarity NPC477326
0.6528 Remote Similarity NPC150557
0.6528 Remote Similarity NPC477323
0.6528 Remote Similarity NPC316807
0.6528 Remote Similarity NPC281563
0.6528 Remote Similarity NPC146380
0.6528 Remote Similarity NPC477320
0.6528 Remote Similarity NPC272841
0.6522 Remote Similarity NPC248427
0.6471 Remote Similarity NPC111882
0.6471 Remote Similarity NPC88278
0.6471 Remote Similarity NPC227707
0.6471 Remote Similarity NPC99573
0.6471 Remote Similarity NPC102981
0.6438 Remote Similarity NPC158302
0.6438 Remote Similarity NPC477346
0.6438 Remote Similarity NPC146992
0.6438 Remote Similarity NPC477344
0.6438 Remote Similarity NPC22742
0.6438 Remote Similarity NPC85759
0.6438 Remote Similarity NPC294748
0.6438 Remote Similarity NPC170595
0.6429 Remote Similarity NPC138273
0.64 Remote Similarity NPC473991
0.6364 Remote Similarity NPC129100
0.6364 Remote Similarity NPC291650
0.6364 Remote Similarity NPC322801
0.6351 Remote Similarity NPC471420
0.6351 Remote Similarity NPC267592
0.6351 Remote Similarity NPC163362
0.6351 Remote Similarity NPC127295
0.6351 Remote Similarity NPC100697
0.6327 Remote Similarity NPC313405
0.6301 Remote Similarity NPC98750
0.6296 Remote Similarity NPC62014
0.6267 Remote Similarity NPC16090
0.6267 Remote Similarity NPC472201
0.6267 Remote Similarity NPC123204
0.6267 Remote Similarity NPC259294
0.6267 Remote Similarity NPC477347

  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 NPC23134 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
0.9583 High Similarity NPD904 Phase 3
0.9583 High Similarity NPD905 Approved
0.92 High Similarity NPD893 Approved
0.92 High Similarity NPD889 Approved
0.92 High Similarity NPD895 Approved
0.92 High Similarity NPD890 Clinical (unspecified phase)
0.92 High Similarity NPD887 Approved
0.92 High Similarity NPD894 Approved
0.92 High Similarity NPD891 Phase 3
0.92 High Similarity NPD888 Phase 3
0.92 High Similarity NPD892 Phase 3
0.9 High Similarity NPD2269 Approved
0.8936 High Similarity NPD8998 Phase 2
0.8936 High Similarity NPD8999 Phase 3
0.8936 High Similarity NPD9000 Phase 3
0.8936 High Similarity NPD8997 Approved
0.8936 High Similarity NPD8993 Phase 1
0.8571 High Similarity NPD8965 Approved
0.8571 High Similarity NPD8966 Approved
0.8333 Intermediate Similarity NPD2267 Suspended
0.8298 Intermediate Similarity NPD8788 Approved
0.807 Intermediate Similarity NPD6123 Approved
0.7797 Intermediate Similarity NPD847 Phase 1
0.7778 Intermediate Similarity NPD9036 Phase 3
0.7778 Intermediate Similarity NPD9035 Clinical (unspecified phase)
0.7755 Intermediate Similarity NPD9006 Approved
0.7636 Intermediate Similarity NPD7346 Approved
0.7544 Intermediate Similarity NPD369 Approved
0.7377 Intermediate Similarity NPD1457 Discontinued
0.7302 Intermediate Similarity NPD896 Approved
0.7302 Intermediate Similarity NPD898 Approved
0.7302 Intermediate Similarity NPD897 Approved
0.7255 Intermediate Similarity NPD9219 Approved
0.7255 Intermediate Similarity NPD9218 Clinical (unspecified phase)
0.7115 Intermediate Similarity NPD8994 Approved
0.6897 Remote Similarity NPD885 Approved
0.6897 Remote Similarity NPD884 Clinical (unspecified phase)
0.6863 Remote Similarity NPD8958 Phase 2
0.6863 Remote Similarity NPD8957 Approved
0.6809 Remote Similarity NPD9052 Approved
0.6809 Remote Similarity NPD9053 Approved
0.6809 Remote Similarity NPD9051 Approved
0.6765 Remote Similarity NPD3181 Approved
0.6667 Remote Similarity NPD9050 Approved
0.6667 Remote Similarity NPD9049 Discontinued
0.6667 Remote Similarity NPD8961 Approved
0.6567 Remote Similarity NPD9445 Approved
0.6491 Remote Similarity NPD1399 Approved
0.6491 Remote Similarity NPD1400 Approved
0.6471 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6471 Remote Similarity NPD8995 Clinical (unspecified phase)
0.6471 Remote Similarity NPD8996 Phase 3
0.6438 Remote Similarity NPD7329 Approved
0.6364 Remote Similarity NPD9033 Approved
0.6364 Remote Similarity NPD9032 Approved
0.6364 Remote Similarity NPD9031 Approved
0.6364 Remote Similarity NPD9030 Approved
0.6346 Remote Similarity NPD8967 Approved
0.6286 Remote Similarity NPD389 Phase 3
0.625 Remote Similarity NPD9139 Approved
0.6197 Remote Similarity NPD1810 Approved
0.6197 Remote Similarity NPD1811 Approved
0.617 Remote Similarity NPD8814 Phase 3
0.6129 Remote Similarity NPD8959 Approved
0.6027 Remote Similarity NPD372 Clinical (unspecified phase)
0.6026 Remote Similarity NPD361 Discontinued
0.6 Remote Similarity NPD370 Phase 3
0.5946 Remote Similarity NPD9435 Approved
0.5946 Remote Similarity NPD9434 Approved
0.5902 Remote Similarity NPD3728 Approved
0.5902 Remote Similarity NPD3730 Approved
0.5849 Remote Similarity NPD7536 Approved
0.5833 Remote Similarity NPD9034 Approved
0.5833 Remote Similarity NPD67 Phase 2
0.5821 Remote Similarity NPD371 Approved
0.5679 Remote Similarity NPD3200 Clinical (unspecified phase)
0.561 Remote Similarity NPD3207 Approved
0.561 Remote Similarity NPD3202 Approved
0.561 Remote Similarity NPD2698 Approved
0.561 Remote Similarity NPD3209 Approved
0.561 Remote Similarity NPD3208 Approved
0.561 Remote Similarity NPD3203 Approved
0.561 Remote Similarity NPD3201 Approved
0.5606 Remote Similarity NPD393 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