Structure

Physi-Chem Properties

Molecular Weight:  346.13
Volume:  310.246
LogP:  -0.793
LogD:  -0.58
LogS:  -1.38
# Rotatable Bonds:  3
TPSA:  141.37
# H-Bond Aceptor:  9
# H-Bond Donor:  5
# Rings:  4
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.349
Synthetic Accessibility Score:  5.146
Fsp3:  0.867
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:  -6.002
MDCK Permeability:  0.00010063752415589988
Pgp-inhibitor:  0.002
Pgp-substrate:  0.976
Human Intestinal Absorption (HIA):  0.903
20% Bioavailability (F20%):  0.008
30% Bioavailability (F30%):  0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.214
Plasma Protein Binding (PPB):  21.329896926879883%
Volume Distribution (VD):  0.395
Pgp-substrate:  56.93511199951172%

ADMET: Metabolism

CYP1A2-inhibitor:  0.013
CYP1A2-substrate:  0.08
CYP2C19-inhibitor:  0.012
CYP2C19-substrate:  0.471
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.029
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.12
CYP3A4-inhibitor:  0.017
CYP3A4-substrate:  0.037

ADMET: Excretion

Clearance (CL):  1.643
Half-life (T1/2):  0.813

ADMET: Toxicity

hERG Blockers:  0.045
Human Hepatotoxicity (H-HT):  0.243
Drug-inuced Liver Injury (DILI):  0.184
AMES Toxicity:  0.167
Rat Oral Acute Toxicity:  0.179
Maximum Recommended Daily Dose:  0.029
Skin Sensitization:  0.236
Carcinogencity:  0.843
Eye Corrosion:  0.003
Eye Irritation:  0.025
Respiratory Toxicity:  0.961

Download Data

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

  Natural Product: NPC148534

Natural Product ID:  NPC148534
Common Name*:   Jioglutoside A
IUPAC Name:   (2S,3R,4R,5R,6S)-2-[[(1bS,2S,5aR,6S)-6-hydroxy-1a-(hydroxymethyl)-2,5a,6,6a-tetrahydro-1bH-oxireno[5,6]cyclopenta[1,3-c]pyran-2-yl]oxy]-6-methyloxane-3,4,5-triol
Synonyms:  
Standard InCHIKey:  QMBUXWAVZQWFED-KKFMILEYSA-N
Standard InCHI:  InChI=1S/C15H22O9/c1-5-8(17)10(19)11(20)14(22-5)23-13-7-6(2-3-21-13)9(18)12-15(7,4-16)24-12/h2-3,5-14,16-20H,4H2,1H3/t5-,6+,7+,8-,9-,10+,11+,12?,13-,14-,15?/m0/s1
SMILES:  C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@H]1[C@H]2[C@@H](C=CO1)[C@@H](C1C2(CO)O1)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3809140
PubChem CID:   11968647
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
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota Roots n.a. n.a. PMID[22916954]
NPO40316 Rehmannia chingii Species Orobanchaceae Eukaryota n.a. n.a. n.a. PMID[26859776]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8101 Rehmannia glutinosa Species Orobanchaceae 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
NPT179 Cell Line A2780 Homo sapiens IC50 > 10000.0 nM PMID[510658]
NPT139 Cell Line HT-29 Homo sapiens IC50 > 10000.0 nM PMID[510658]
NPT81 Cell Line A549 Homo sapiens IC50 > 10000.0 nM PMID[510658]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 10000.0 nM PMID[510658]

☑ 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 NPC148534 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
0.988 High Similarity NPC22918
0.9878 High Similarity NPC258501
0.9512 High Similarity NPC259296
0.9512 High Similarity NPC98276
0.9419 High Similarity NPC276298
0.9286 High Similarity NPC149018
0.9286 High Similarity NPC171484
0.8966 High Similarity NPC50464
0.8764 High Similarity NPC274274
0.8764 High Similarity NPC473150
0.8764 High Similarity NPC294643
0.8539 High Similarity NPC93190
0.8495 Intermediate Similarity NPC470684
0.8495 Intermediate Similarity NPC470683
0.7812 Intermediate Similarity NPC284063
0.7778 Intermediate Similarity NPC220167
0.7778 Intermediate Similarity NPC136699
0.7767 Intermediate Similarity NPC193741
0.7732 Intermediate Similarity NPC86843
0.7708 Intermediate Similarity NPC6765
0.7708 Intermediate Similarity NPC93869
0.77 Intermediate Similarity NPC329834
0.7674 Intermediate Similarity NPC279575
0.7619 Intermediate Similarity NPC475924
0.7619 Intermediate Similarity NPC475851
0.7614 Intermediate Similarity NPC170595
0.7604 Intermediate Similarity NPC274588
0.7579 Intermediate Similarity NPC235051
0.7549 Intermediate Similarity NPC127235
0.7529 Intermediate Similarity NPC470660
0.7529 Intermediate Similarity NPC470659
0.75 Intermediate Similarity NPC216911
0.75 Intermediate Similarity NPC476228
0.75 Intermediate Similarity NPC280390
0.7476 Intermediate Similarity NPC148270
0.7476 Intermediate Similarity NPC197813
0.7476 Intermediate Similarity NPC80338
0.7449 Intermediate Similarity NPC170527
0.74 Intermediate Similarity NPC476320
0.74 Intermediate Similarity NPC476211
0.7396 Intermediate Similarity NPC66504
0.7379 Intermediate Similarity NPC170432
0.7368 Intermediate Similarity NPC299527
0.7353 Intermediate Similarity NPC475928
0.7353 Intermediate Similarity NPC37240
0.7327 Intermediate Similarity NPC27474
0.7327 Intermediate Similarity NPC287539
0.7327 Intermediate Similarity NPC3488
0.7327 Intermediate Similarity NPC476230
0.7326 Intermediate Similarity NPC248427
0.7255 Intermediate Similarity NPC4899
0.7255 Intermediate Similarity NPC304163
0.7255 Intermediate Similarity NPC474730
0.7255 Intermediate Similarity NPC177013
0.7255 Intermediate Similarity NPC35185
0.7245 Intermediate Similarity NPC63897
0.7238 Intermediate Similarity NPC110701
0.7228 Intermediate Similarity NPC244878
0.7212 Intermediate Similarity NPC474569
0.72 Intermediate Similarity NPC76486
0.7184 Intermediate Similarity NPC329704
0.7157 Intermediate Similarity NPC20673
0.7129 Intermediate Similarity NPC37866
0.7129 Intermediate Similarity NPC151093
0.7128 Intermediate Similarity NPC470658
0.7115 Intermediate Similarity NPC312774
0.71 Intermediate Similarity NPC161293
0.7097 Intermediate Similarity NPC260852
0.7064 Intermediate Similarity NPC287075
0.7059 Intermediate Similarity NPC91497
0.7054 Intermediate Similarity NPC219656
0.7048 Intermediate Similarity NPC26798
0.7041 Intermediate Similarity NPC48463
0.703 Intermediate Similarity NPC261372
0.703 Intermediate Similarity NPC263674
0.703 Intermediate Similarity NPC58267
0.701 Intermediate Similarity NPC104129
0.701 Intermediate Similarity NPC249408
0.7009 Intermediate Similarity NPC40440
0.7009 Intermediate Similarity NPC42482
0.7 Intermediate Similarity NPC291709
0.7 Intermediate Similarity NPC241407
0.699 Remote Similarity NPC31346
0.699 Remote Similarity NPC219038
0.699 Remote Similarity NPC98859
0.699 Remote Similarity NPC4637
0.6989 Remote Similarity NPC20072
0.6981 Remote Similarity NPC226642
0.6972 Remote Similarity NPC19888
0.6964 Remote Similarity NPC472080
0.6961 Remote Similarity NPC158088
0.6961 Remote Similarity NPC223700
0.6961 Remote Similarity NPC96399
0.6961 Remote Similarity NPC469918
0.6961 Remote Similarity NPC469919
0.6961 Remote Similarity NPC157739
0.6961 Remote Similarity NPC117066
0.6957 Remote Similarity NPC100697
0.6952 Remote Similarity NPC475521
0.6952 Remote Similarity NPC474464
0.6952 Remote Similarity NPC475365
0.6939 Remote Similarity NPC197107
0.6939 Remote Similarity NPC117596
0.6931 Remote Similarity NPC472989
0.6931 Remote Similarity NPC207617
0.693 Remote Similarity NPC233500
0.6923 Remote Similarity NPC106668
0.6923 Remote Similarity NPC136816
0.6923 Remote Similarity NPC272015
0.6923 Remote Similarity NPC471599
0.6916 Remote Similarity NPC7213
0.6907 Remote Similarity NPC248312
0.6893 Remote Similarity NPC471247
0.6887 Remote Similarity NPC181845
0.6887 Remote Similarity NPC242748
0.6887 Remote Similarity NPC474015
0.6887 Remote Similarity NPC473923
0.6887 Remote Similarity NPC473476
0.6881 Remote Similarity NPC477032
0.6881 Remote Similarity NPC477028
0.6881 Remote Similarity NPC124677
0.6881 Remote Similarity NPC197231
0.687 Remote Similarity NPC196130
0.6869 Remote Similarity NPC472124
0.6869 Remote Similarity NPC472126
0.6869 Remote Similarity NPC472125
0.6863 Remote Similarity NPC153559
0.6863 Remote Similarity NPC278939
0.6863 Remote Similarity NPC471770
0.6863 Remote Similarity NPC347923
0.6863 Remote Similarity NPC473890
0.6863 Remote Similarity NPC476057
0.6863 Remote Similarity NPC473555
0.6863 Remote Similarity NPC472290
0.6863 Remote Similarity NPC243728
0.6857 Remote Similarity NPC27687
0.6857 Remote Similarity NPC475701
0.6852 Remote Similarity NPC472901
0.6852 Remote Similarity NPC208307
0.6842 Remote Similarity NPC116613
0.6842 Remote Similarity NPC474156
0.6832 Remote Similarity NPC240838
0.6827 Remote Similarity NPC47566
0.6827 Remote Similarity NPC4831
0.6827 Remote Similarity NPC267510
0.6827 Remote Similarity NPC129372
0.6827 Remote Similarity NPC88000
0.6827 Remote Similarity NPC160734
0.6827 Remote Similarity NPC309425
0.6827 Remote Similarity NPC472023
0.6827 Remote Similarity NPC470168
0.6822 Remote Similarity NPC230507
0.6822 Remote Similarity NPC14704
0.6822 Remote Similarity NPC305423
0.6822 Remote Similarity NPC33053
0.6822 Remote Similarity NPC94272
0.6822 Remote Similarity NPC283829
0.6822 Remote Similarity NPC161676
0.6822 Remote Similarity NPC470432
0.6822 Remote Similarity NPC473469
0.6822 Remote Similarity NPC113044
0.6818 Remote Similarity NPC254255
0.6818 Remote Similarity NPC473567
0.6818 Remote Similarity NPC216595
0.6818 Remote Similarity NPC308140
0.6813 Remote Similarity NPC188793
0.681 Remote Similarity NPC219804
0.6804 Remote Similarity NPC31349
0.68 Remote Similarity NPC470187
0.68 Remote Similarity NPC61201
0.6796 Remote Similarity NPC474957
0.6796 Remote Similarity NPC79449
0.6796 Remote Similarity NPC473307
0.6796 Remote Similarity NPC90819
0.6796 Remote Similarity NPC124181
0.6796 Remote Similarity NPC312325
0.6796 Remote Similarity NPC274458
0.6792 Remote Similarity NPC471111
0.6792 Remote Similarity NPC470885
0.6792 Remote Similarity NPC187400
0.6792 Remote Similarity NPC221562
0.6768 Remote Similarity NPC307699
0.6765 Remote Similarity NPC474297
0.6765 Remote Similarity NPC241911
0.6762 Remote Similarity NPC13171
0.6762 Remote Similarity NPC195510
0.6762 Remote Similarity NPC214714
0.6762 Remote Similarity NPC200672
0.6762 Remote Similarity NPC154452
0.6759 Remote Similarity NPC295980
0.6759 Remote Similarity NPC472897
0.6759 Remote Similarity NPC475634
0.6759 Remote Similarity NPC472896
0.6759 Remote Similarity NPC98696
0.6759 Remote Similarity NPC476541
0.6759 Remote Similarity NPC476539
0.6759 Remote Similarity NPC476538
0.6759 Remote Similarity NPC235824
0.6759 Remote Similarity NPC476540
0.6757 Remote Similarity NPC476546

  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 NPC148534 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
0.6638 Remote Similarity NPD7503 Approved
0.6364 Remote Similarity NPD6412 Phase 2
0.6364 Remote Similarity NPD4249 Approved
0.6356 Remote Similarity NPD8033 Approved
0.63 Remote Similarity NPD4251 Approved
0.63 Remote Similarity NPD4250 Approved
0.6239 Remote Similarity NPD7327 Approved
0.6239 Remote Similarity NPD7328 Approved
0.6186 Remote Similarity NPD7516 Approved
0.6154 Remote Similarity NPD8171 Discontinued
0.6139 Remote Similarity NPD7524 Approved
0.6134 Remote Similarity NPD8377 Approved
0.6134 Remote Similarity NPD8294 Approved
0.6083 Remote Similarity NPD8379 Approved
0.6083 Remote Similarity NPD8335 Approved
0.6083 Remote Similarity NPD8380 Approved
0.6083 Remote Similarity NPD8378 Approved
0.6083 Remote Similarity NPD8296 Approved
0.6034 Remote Similarity NPD8133 Approved
0.6 Remote Similarity NPD7338 Clinical (unspecified phase)
0.5918 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5902 Remote Similarity NPD6370 Approved
0.59 Remote Similarity NPD6695 Phase 3
0.5887 Remote Similarity NPD7507 Approved
0.5877 Remote Similarity NPD6686 Approved
0.5862 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5812 Remote Similarity NPD6053 Discontinued
0.581 Remote Similarity NPD46 Approved
0.581 Remote Similarity NPD7838 Discovery
0.581 Remote Similarity NPD3168 Discontinued
0.581 Remote Similarity NPD6698 Approved
0.5789 Remote Similarity NPD1811 Approved
0.5789 Remote Similarity NPD1810 Approved
0.5783 Remote Similarity NPD891 Phase 3
0.5783 Remote Similarity NPD895 Approved
0.5783 Remote Similarity NPD894 Approved
0.5783 Remote Similarity NPD890 Clinical (unspecified phase)
0.5783 Remote Similarity NPD893 Approved
0.5783 Remote Similarity NPD889 Approved
0.5783 Remote Similarity NPD887 Approved
0.5783 Remote Similarity NPD888 Phase 3
0.5783 Remote Similarity NPD892 Phase 3
0.5758 Remote Similarity NPD4819 Approved
0.5758 Remote Similarity NPD4822 Approved
0.5758 Remote Similarity NPD4821 Approved
0.5758 Remote Similarity NPD4820 Approved
0.5748 Remote Similarity NPD7319 Approved
0.5738 Remote Similarity NPD6054 Approved
0.5732 Remote Similarity NPD904 Phase 3
0.5732 Remote Similarity NPD905 Approved
0.5727 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5714 Remote Similarity NPD4268 Approved
0.5714 Remote Similarity NPD4271 Approved
0.5691 Remote Similarity NPD6015 Approved
0.5691 Remote Similarity NPD8513 Phase 3
0.5691 Remote Similarity NPD6016 Approved
0.5673 Remote Similarity NPD7750 Discontinued
0.567 Remote Similarity NPD6933 Approved
0.5669 Remote Similarity NPD7736 Approved
0.5645 Remote Similarity NPD5988 Approved
0.5644 Remote Similarity NPD6435 Approved
0.5638 Remote Similarity NPD7532 Clinical (unspecified phase)
0.5625 Remote Similarity NPD5344 Discontinued
0.5615 Remote Similarity NPD8449 Approved
0.5614 Remote Similarity NPD4056 Clinical (unspecified phase)
0.5614 Remote Similarity NPD8170 Clinical (unspecified phase)
0.5614 Remote Similarity NPD4057 Clinical (unspecified phase)
0.5612 Remote Similarity NPD6932 Approved
0.561 Remote Similarity NPD6319 Approved
0.561 Remote Similarity NPD6059 Approved
0.56 Remote Similarity NPD6930 Phase 2
0.56 Remote Similarity NPD6928 Phase 2
0.56 Remote Similarity NPD6931 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