Structure

Physi-Chem Properties

Molecular Weight:  262.14
Volume:  257.657
LogP:  0.152
LogD:  -0.086
LogS:  -0.972
# Rotatable Bonds:  6
TPSA:  99.38
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.368
Synthetic Accessibility Score:  3.84
Fsp3:  0.833
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:  -5.058
MDCK Permeability:  0.0002952426439151168
Pgp-inhibitor:  0.065
Pgp-substrate:  0.016
Human Intestinal Absorption (HIA):  0.897
20% Bioavailability (F20%):  0.879
30% Bioavailability (F30%):  0.962

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.351
Plasma Protein Binding (PPB):  51.51093673706055%
Volume Distribution (VD):  0.546
Pgp-substrate:  37.671504974365234%

ADMET: Metabolism

CYP1A2-inhibitor:  0.021
CYP1A2-substrate:  0.084
CYP2C19-inhibitor:  0.018
CYP2C19-substrate:  0.305
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.206
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.126
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.04

ADMET: Excretion

Clearance (CL):  1.884
Half-life (T1/2):  0.872

ADMET: Toxicity

hERG Blockers:  0.028
Human Hepatotoxicity (H-HT):  0.042
Drug-inuced Liver Injury (DILI):  0.012
AMES Toxicity:  0.066
Rat Oral Acute Toxicity:  0.043
Maximum Recommended Daily Dose:  0.003
Skin Sensitization:  0.657
Carcinogencity:  0.053
Eye Corrosion:  0.018
Eye Irritation:  0.838
Respiratory Toxicity:  0.032

Download Data

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

  Natural Product: NPC294813

Natural Product ID:  NPC294813
Common Name*:   3-Hexenyl-Beta-D-Glucopyranoside
IUPAC Name:   (2R,3R,4S,5S,6R)-2-[(E)-hex-3-enoxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms:  
Standard InCHIKey:  OZIPFYKAIOOVEJ-WQPBHKFLSA-N
Standard InCHI:  InChI=1S/C12H22O6/c1-2-3-4-5-6-17-12-11(16)10(15)9(14)8(7-13)18-12/h3-4,8-16H,2,5-7H2,1H3/b4-3+/t8-,9-,10+,11-,12-/m1/s1
SMILES:  CC/C=C/CCO[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2152486
PubChem CID:   5318046
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001766] Fatty acyl glycosides
          • [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

*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
NPO10900 Cinnamomum subavenium Species Lauraceae Eukaryota stems Wulai Hsiang, Taipei County, Taiwan 2005-MAY PMID[17253858]
NPO10900 Cinnamomum subavenium Species Lauraceae Eukaryota Leaves n.a. n.a. PMID[23025417]
NPO10900 Cinnamomum subavenium Species Lauraceae Eukaryota stem bark Laifeng, Hubei Province, China 2012-JUL PMID[26087384]
NPO10900 Cinnamomum subavenium Species Lauraceae 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
NPT2 Others Unspecified IC50 > 150000.0 nM PMID[505506]

☑ 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 NPC294813 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 NPC13143
0.8852 High Similarity NPC155457
0.8676 High Similarity NPC472174
0.8571 High Similarity NPC277570
0.8529 High Similarity NPC132938
0.8438 Intermediate Similarity NPC31496
0.8406 Intermediate Similarity NPC472173
0.8308 Intermediate Similarity NPC147292
0.8261 Intermediate Similarity NPC55652
0.8194 Intermediate Similarity NPC133377
0.8169 Intermediate Similarity NPC229655
0.8169 Intermediate Similarity NPC326661
0.8056 Intermediate Similarity NPC110813
0.7971 Intermediate Similarity NPC474078
0.7966 Intermediate Similarity NPC233726
0.7966 Intermediate Similarity NPC23134
0.7966 Intermediate Similarity NPC124963
0.7867 Intermediate Similarity NPC280367
0.7763 Intermediate Similarity NPC251026
0.7667 Intermediate Similarity NPC326533
0.7662 Intermediate Similarity NPC473315
0.7662 Intermediate Similarity NPC142111
0.7632 Intermediate Similarity NPC469469
0.7632 Intermediate Similarity NPC21693
0.7632 Intermediate Similarity NPC236649
0.7627 Intermediate Similarity NPC157193
0.7627 Intermediate Similarity NPC282143
0.7627 Intermediate Similarity NPC299781
0.7627 Intermediate Similarity NPC42503
0.7581 Intermediate Similarity NPC303727
0.7564 Intermediate Similarity NPC473308
0.75 Intermediate Similarity NPC163362
0.75 Intermediate Similarity NPC127295
0.75 Intermediate Similarity NPC100697
0.7458 Intermediate Similarity NPC14144
0.7436 Intermediate Similarity NPC470313
0.7436 Intermediate Similarity NPC473500
0.7436 Intermediate Similarity NPC38295
0.7436 Intermediate Similarity NPC156089
0.7419 Intermediate Similarity NPC323361
0.7419 Intermediate Similarity NPC157514
0.7419 Intermediate Similarity NPC89145
0.7419 Intermediate Similarity NPC165198
0.7419 Intermediate Similarity NPC58629
0.7419 Intermediate Similarity NPC242073
0.7419 Intermediate Similarity NPC269166
0.7419 Intermediate Similarity NPC246558
0.7419 Intermediate Similarity NPC130683
0.7419 Intermediate Similarity NPC145112
0.7419 Intermediate Similarity NPC67660
0.7419 Intermediate Similarity NPC107914
0.7375 Intermediate Similarity NPC208473
0.7344 Intermediate Similarity NPC148424
0.7342 Intermediate Similarity NPC266718
0.7342 Intermediate Similarity NPC220167
0.7342 Intermediate Similarity NPC475035
0.7342 Intermediate Similarity NPC136699
0.7308 Intermediate Similarity NPC20072
0.7288 Intermediate Similarity NPC321087
0.7288 Intermediate Similarity NPC277475
0.725 Intermediate Similarity NPC470658
0.725 Intermediate Similarity NPC73166
0.725 Intermediate Similarity NPC470124
0.7231 Intermediate Similarity NPC219040
0.7231 Intermediate Similarity NPC472025
0.7213 Intermediate Similarity NPC323574
0.7195 Intermediate Similarity NPC470137
0.7121 Intermediate Similarity NPC320032
0.7121 Intermediate Similarity NPC322855
0.7119 Intermediate Similarity NPC73906
0.7119 Intermediate Similarity NPC285364
0.7119 Intermediate Similarity NPC176017
0.7119 Intermediate Similarity NPC289758
0.7119 Intermediate Similarity NPC199857
0.7119 Intermediate Similarity NPC69445
0.7119 Intermediate Similarity NPC165846
0.7119 Intermediate Similarity NPC21209
0.7119 Intermediate Similarity NPC92246
0.7119 Intermediate Similarity NPC255377
0.7073 Intermediate Similarity NPC118077
0.7073 Intermediate Similarity NPC475186
0.7073 Intermediate Similarity NPC125142
0.7073 Intermediate Similarity NPC475037
0.7049 Intermediate Similarity NPC82512
0.7037 Intermediate Similarity NPC477747
0.7037 Intermediate Similarity NPC477746
0.7024 Intermediate Similarity NPC473311
0.7024 Intermediate Similarity NPC327253
0.7015 Intermediate Similarity NPC143326
0.6988 Remote Similarity NPC471756
0.6988 Remote Similarity NPC471755
0.6988 Remote Similarity NPC137368
0.6962 Remote Similarity NPC16090
0.6951 Remote Similarity NPC470836
0.6941 Remote Similarity NPC182632
0.6941 Remote Similarity NPC282705
0.6923 Remote Similarity NPC179933
0.6914 Remote Similarity NPC98276
0.6914 Remote Similarity NPC259296
0.6912 Remote Similarity NPC477762
0.6912 Remote Similarity NPC472026
0.6912 Remote Similarity NPC477755
0.6912 Remote Similarity NPC477750
0.6912 Remote Similarity NPC477753
0.6912 Remote Similarity NPC477763
0.6912 Remote Similarity NPC477757
0.6905 Remote Similarity NPC249408
0.6905 Remote Similarity NPC104129
0.6905 Remote Similarity NPC285588
0.6883 Remote Similarity NPC474026
0.6866 Remote Similarity NPC290179
0.6866 Remote Similarity NPC34877
0.6866 Remote Similarity NPC317023
0.686 Remote Similarity NPC320552
0.686 Remote Similarity NPC61201
0.6829 Remote Similarity NPC475034
0.6824 Remote Similarity NPC43074
0.6824 Remote Similarity NPC139782
0.6824 Remote Similarity NPC209047
0.6824 Remote Similarity NPC118078
0.6824 Remote Similarity NPC74672
0.6824 Remote Similarity NPC242503
0.6795 Remote Similarity NPC248775
0.6786 Remote Similarity NPC248312
0.6782 Remote Similarity NPC262312
0.6782 Remote Similarity NPC70323
0.6782 Remote Similarity NPC23454
0.6782 Remote Similarity NPC35269
0.678 Remote Similarity NPC70756
0.678 Remote Similarity NPC320240
0.6744 Remote Similarity NPC263545
0.6744 Remote Similarity NPC473950
0.6744 Remote Similarity NPC61894
0.6744 Remote Similarity NPC473604
0.6744 Remote Similarity NPC309898
0.6744 Remote Similarity NPC186840
0.6744 Remote Similarity NPC473581
0.6744 Remote Similarity NPC15851
0.6744 Remote Similarity NPC9447
0.6744 Remote Similarity NPC475603
0.6744 Remote Similarity NPC475125
0.6744 Remote Similarity NPC472199
0.6744 Remote Similarity NPC469410
0.6744 Remote Similarity NPC110072
0.6744 Remote Similarity NPC472197
0.6744 Remote Similarity NPC111567
0.6721 Remote Similarity NPC252918
0.6721 Remote Similarity NPC230789
0.6714 Remote Similarity NPC325773
0.6711 Remote Similarity NPC24590
0.6709 Remote Similarity NPC470148
0.6709 Remote Similarity NPC470149
0.6709 Remote Similarity NPC180725
0.6706 Remote Similarity NPC477748
0.6667 Remote Similarity NPC238090
0.6667 Remote Similarity NPC474792
0.6667 Remote Similarity NPC81896
0.6667 Remote Similarity NPC67398
0.6667 Remote Similarity NPC258788
0.6667 Remote Similarity NPC472196
0.6667 Remote Similarity NPC475711
0.6667 Remote Similarity NPC321919
0.6667 Remote Similarity NPC91654
0.6667 Remote Similarity NPC280390
0.6667 Remote Similarity NPC472195
0.6629 Remote Similarity NPC45313
0.6628 Remote Similarity NPC202886
0.6628 Remote Similarity NPC6414
0.6628 Remote Similarity NPC159876
0.6628 Remote Similarity NPC303451
0.6625 Remote Similarity NPC470147
0.6625 Remote Similarity NPC133226
0.6623 Remote Similarity NPC473948
0.662 Remote Similarity NPC475221
0.661 Remote Similarity NPC86191
0.661 Remote Similarity NPC291502
0.661 Remote Similarity NPC317182
0.661 Remote Similarity NPC213159
0.661 Remote Similarity NPC134252
0.661 Remote Similarity NPC298699
0.6591 Remote Similarity NPC472198
0.6591 Remote Similarity NPC477927
0.6591 Remote Similarity NPC305160
0.6591 Remote Similarity NPC3568
0.6591 Remote Similarity NPC17290
0.6591 Remote Similarity NPC72817
0.6591 Remote Similarity NPC2003
0.6591 Remote Similarity NPC294293
0.6591 Remote Similarity NPC192066
0.6591 Remote Similarity NPC54961
0.6591 Remote Similarity NPC159698
0.6591 Remote Similarity NPC158445
0.6591 Remote Similarity NPC156782
0.6591 Remote Similarity NPC25701
0.6591 Remote Similarity NPC157353
0.6591 Remote Similarity NPC282088
0.6591 Remote Similarity NPC256570
0.6588 Remote Similarity NPC148534
0.6575 Remote Similarity NPC25298
0.6562 Remote Similarity NPC200772

  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 NPC294813 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
0.7667 Intermediate Similarity NPD904 Phase 3
0.7667 Intermediate Similarity NPD905 Approved
0.7419 Intermediate Similarity NPD893 Approved
0.7419 Intermediate Similarity NPD887 Approved
0.7419 Intermediate Similarity NPD895 Approved
0.7419 Intermediate Similarity NPD890 Clinical (unspecified phase)
0.7419 Intermediate Similarity NPD889 Approved
0.7419 Intermediate Similarity NPD892 Phase 3
0.7419 Intermediate Similarity NPD888 Phase 3
0.7419 Intermediate Similarity NPD894 Approved
0.7419 Intermediate Similarity NPD891 Phase 3
0.7258 Intermediate Similarity NPD2269 Approved
0.7119 Intermediate Similarity NPD8993 Phase 1
0.7119 Intermediate Similarity NPD9000 Phase 3
0.7119 Intermediate Similarity NPD8997 Approved
0.7119 Intermediate Similarity NPD8998 Phase 2
0.7119 Intermediate Similarity NPD8999 Phase 3
0.6885 Remote Similarity NPD8965 Approved
0.6885 Remote Similarity NPD8966 Approved
0.6824 Remote Similarity NPD8522 Clinical (unspecified phase)
0.6818 Remote Similarity NPD2267 Suspended
0.6667 Remote Similarity NPD6123 Approved
0.661 Remote Similarity NPD8788 Approved
0.6479 Remote Similarity NPD847 Phase 1
0.6377 Remote Similarity NPD585 Clinical (unspecified phase)
0.6364 Remote Similarity NPD9036 Phase 3
0.6364 Remote Similarity NPD9035 Clinical (unspecified phase)
0.6269 Remote Similarity NPD7346 Approved
0.6232 Remote Similarity NPD369 Approved
0.623 Remote Similarity NPD9006 Approved
0.6164 Remote Similarity NPD1457 Discontinued
0.6133 Remote Similarity NPD896 Approved
0.6133 Remote Similarity NPD897 Approved
0.6133 Remote Similarity NPD898 Approved
0.5915 Remote Similarity NPD6109 Phase 1
0.5889 Remote Similarity NPD6698 Approved
0.5889 Remote Similarity NPD46 Approved
0.5873 Remote Similarity NPD9218 Clinical (unspecified phase)
0.5873 Remote Similarity NPD9219 Approved
0.5789 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5781 Remote Similarity NPD8994 Approved
0.575 Remote Similarity NPD3181 Approved
0.5714 Remote Similarity NPD7838 Discovery
0.5714 Remote Similarity NPD885 Approved
0.5714 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5714 Remote Similarity NPD884 Clinical (unspecified phase)
0.5714 Remote Similarity NPD1407 Approved
0.57 Remote Similarity NPD6412 Phase 2
0.5652 Remote Similarity NPD7983 Approved
0.5644 Remote Similarity NPD6686 Approved
0.56 Remote Similarity NPD8961 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