Structure

Physi-Chem Properties

Molecular Weight:  410.18
Volume:  379.531
LogP:  -1.304
LogD:  -1.806
LogS:  -0.607
# Rotatable Bonds:  8
TPSA:  178.53
# H-Bond Aceptor:  11
# H-Bond Donor:  7
# Rings:  2
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.198
Synthetic Accessibility Score:  4.471
Fsp3:  0.882
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.878
MDCK Permeability:  0.0001250882778549567
Pgp-inhibitor:  0.006
Pgp-substrate:  0.295
Human Intestinal Absorption (HIA):  0.976
20% Bioavailability (F20%):  0.891
30% Bioavailability (F30%):  0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.183
Plasma Protein Binding (PPB):  26.913738250732422%
Volume Distribution (VD):  0.42
Pgp-substrate:  59.762794494628906%

ADMET: Metabolism

CYP1A2-inhibitor:  0.007
CYP1A2-substrate:  0.038
CYP2C19-inhibitor:  0.013
CYP2C19-substrate:  0.095
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.032
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.094
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.01

ADMET: Excretion

Clearance (CL):  1.007
Half-life (T1/2):  0.844

ADMET: Toxicity

hERG Blockers:  0.242
Human Hepatotoxicity (H-HT):  0.048
Drug-inuced Liver Injury (DILI):  0.019
AMES Toxicity:  0.156
Rat Oral Acute Toxicity:  0.072
Maximum Recommended Daily Dose:  0.001
Skin Sensitization:  0.305
Carcinogencity:  0.133
Eye Corrosion:  0.005
Eye Irritation:  0.256
Respiratory Toxicity:  0.02

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

  Natural Product: NPC147292

Natural Product ID:  NPC147292
Common Name*:   3-Methylbut-3-Enyl-6-O-Beta-D-Glucopyranosyl-Beta-D-Glucopyranose
IUPAC Name:   (2R,3S,4S,5R,6R)-2-(hydroxymethyl)-6-[[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-(3-methylbut-3-enoxy)oxan-2-yl]methoxy]oxane-3,4,5-triol
Synonyms:  
Standard InCHIKey:  KNJRIEFLSCUKAY-BNTHRHBTSA-N
Standard InCHI:  InChI=1S/C17H30O11/c1-7(2)3-4-25-16-14(23)13(22)11(20)9(28-16)6-26-17-15(24)12(21)10(19)8(5-18)27-17/h8-24H,1,3-6H2,2H3/t8-,9-,10-,11-,12+,13+,14-,15-,16-,17-/m1/s1
SMILES:  OC[C@H]1O[C@@H](OC[C@H]2O[C@@H](OCCC(=C)C)[C@@H]([C@H]([C@@H]2O)O)O)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL226659
PubChem CID:   10179753
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
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. leaf n.a. PMID[11348221]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[15844957]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota fruits n.a. n.a. PMID[16378361]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota fruits Tahiti n.a. PMID[17378609]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[17480098]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota roots n.a. n.a. PMID[18076142]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[24224843]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[27196335]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[32083868]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4323 Morinda citrifolia Species Rubiaceae 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
NPT80 Cell Line Raji Homo sapiens Activity = 60.0 % PMID[479620]
NPT164 Organism Human herpesvirus 4 Human herpesvirus 4 Activity = 14.2 % PMID[479620]
NPT164 Organism Human herpesvirus 4 Human herpesvirus 4 Activity = 58.3 % PMID[479620]
NPT164 Organism Human herpesvirus 4 Human herpesvirus 4 Activity = 85.4 % PMID[479620]
NPT164 Organism Human herpesvirus 4 Human herpesvirus 4 Activity = 100.0 % PMID[479620]

☑ 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 NPC147292 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
0.9333 High Similarity NPC155457
0.8382 Intermediate Similarity NPC474078
0.8333 Intermediate Similarity NPC303727
0.8308 Intermediate Similarity NPC13143
0.8308 Intermediate Similarity NPC294813
0.8226 Intermediate Similarity NPC472025
0.8167 Intermediate Similarity NPC89145
0.8167 Intermediate Similarity NPC145112
0.8167 Intermediate Similarity NPC58629
0.8167 Intermediate Similarity NPC107914
0.8167 Intermediate Similarity NPC269166
0.8167 Intermediate Similarity NPC157514
0.8167 Intermediate Similarity NPC246558
0.8167 Intermediate Similarity NPC67660
0.8167 Intermediate Similarity NPC242073
0.8167 Intermediate Similarity NPC165198
0.803 Intermediate Similarity NPC31496
0.7887 Intermediate Similarity NPC55652
0.7879 Intermediate Similarity NPC277570
0.7867 Intermediate Similarity NPC127295
0.7867 Intermediate Similarity NPC163362
0.7846 Intermediate Similarity NPC477753
0.7846 Intermediate Similarity NPC477750
0.7846 Intermediate Similarity NPC477757
0.7846 Intermediate Similarity NPC477763
0.7846 Intermediate Similarity NPC477762
0.7846 Intermediate Similarity NPC477755
0.7833 Intermediate Similarity NPC326533
0.7833 Intermediate Similarity NPC23134
0.7833 Intermediate Similarity NPC233726
0.7833 Intermediate Similarity NPC124963
0.7812 Intermediate Similarity NPC317023
0.7812 Intermediate Similarity NPC34877
0.7812 Intermediate Similarity NPC290179
0.7662 Intermediate Similarity NPC20072
0.7656 Intermediate Similarity NPC219040
0.7639 Intermediate Similarity NPC132938
0.7581 Intermediate Similarity NPC323361
0.7581 Intermediate Similarity NPC130683
0.7576 Intermediate Similarity NPC472026
0.7568 Intermediate Similarity NPC229655
0.7536 Intermediate Similarity NPC477751
0.7536 Intermediate Similarity NPC477756
0.7536 Intermediate Similarity NPC477752
0.7536 Intermediate Similarity NPC477764
0.7534 Intermediate Similarity NPC472174
0.75 Intermediate Similarity NPC148424
0.75 Intermediate Similarity NPC282143
0.75 Intermediate Similarity NPC42503
0.75 Intermediate Similarity NPC157193
0.75 Intermediate Similarity NPC299781
0.7429 Intermediate Similarity NPC477760
0.7429 Intermediate Similarity NPC477758
0.7429 Intermediate Similarity NPC477754
0.7429 Intermediate Similarity NPC477759
0.7429 Intermediate Similarity NPC477761
0.7403 Intermediate Similarity NPC100697
0.7391 Intermediate Similarity NPC76881
0.7391 Intermediate Similarity NPC12040
0.7391 Intermediate Similarity NPC190418
0.7391 Intermediate Similarity NPC471760
0.7391 Intermediate Similarity NPC471761
0.7375 Intermediate Similarity NPC470124
0.7375 Intermediate Similarity NPC73166
0.7368 Intermediate Similarity NPC133377
0.7333 Intermediate Similarity NPC14144
0.7308 Intermediate Similarity NPC280367
0.7297 Intermediate Similarity NPC472173
0.7246 Intermediate Similarity NPC6848
0.7237 Intermediate Similarity NPC110813
0.7195 Intermediate Similarity NPC475186
0.7195 Intermediate Similarity NPC125142
0.7195 Intermediate Similarity NPC118077
0.7167 Intermediate Similarity NPC321087
0.7167 Intermediate Similarity NPC277475
0.7164 Intermediate Similarity NPC143326
0.7125 Intermediate Similarity NPC470313
0.7125 Intermediate Similarity NPC38295
0.7125 Intermediate Similarity NPC156089
0.7125 Intermediate Similarity NPC473500
0.7108 Intermediate Similarity NPC248312
0.7097 Intermediate Similarity NPC323574
0.7089 Intermediate Similarity NPC16090
0.7083 Intermediate Similarity NPC97736
0.7083 Intermediate Similarity NPC250619
0.7083 Intermediate Similarity NPC50228
0.7083 Intermediate Similarity NPC67099
0.7059 Intermediate Similarity NPC472124
0.7059 Intermediate Similarity NPC472126
0.7059 Intermediate Similarity NPC472125
0.7037 Intermediate Similarity NPC220167
0.7037 Intermediate Similarity NPC259296
0.7037 Intermediate Similarity NPC136699
0.7037 Intermediate Similarity NPC98276
0.7024 Intermediate Similarity NPC285588
0.7015 Intermediate Similarity NPC320032
0.7015 Intermediate Similarity NPC322855
0.7 Intermediate Similarity NPC255377
0.7 Intermediate Similarity NPC69445
0.7 Intermediate Similarity NPC289758
0.7 Intermediate Similarity NPC73906
0.7 Intermediate Similarity NPC199857
0.7 Intermediate Similarity NPC92246
0.7 Intermediate Similarity NPC285364
0.7 Intermediate Similarity NPC165846
0.7 Intermediate Similarity NPC21209
0.7 Intermediate Similarity NPC251026
0.7 Intermediate Similarity NPC176017
0.6986 Remote Similarity NPC211428
0.6986 Remote Similarity NPC285003
0.6986 Remote Similarity NPC241265
0.6951 Remote Similarity NPC477747
0.6951 Remote Similarity NPC470658
0.6951 Remote Similarity NPC477746
0.6951 Remote Similarity NPC34581
0.6941 Remote Similarity NPC120021
0.6941 Remote Similarity NPC327253
0.6941 Remote Similarity NPC307699
0.6941 Remote Similarity NPC117596
0.6941 Remote Similarity NPC270908
0.6941 Remote Similarity NPC470573
0.6941 Remote Similarity NPC216826
0.6941 Remote Similarity NPC231710
0.6941 Remote Similarity NPC65665
0.6935 Remote Similarity NPC82512
0.6914 Remote Similarity NPC142111
0.6914 Remote Similarity NPC473315
0.6905 Remote Similarity NPC471755
0.6905 Remote Similarity NPC471756
0.6905 Remote Similarity NPC137368
0.6892 Remote Similarity NPC52268
0.6892 Remote Similarity NPC53760
0.6883 Remote Similarity NPC326661
0.6875 Remote Similarity NPC236649
0.6875 Remote Similarity NPC469469
0.6875 Remote Similarity NPC21693
0.6867 Remote Similarity NPC470836
0.686 Remote Similarity NPC110072
0.6829 Remote Similarity NPC473308
0.6829 Remote Similarity NPC266718
0.6829 Remote Similarity NPC475035
0.6824 Remote Similarity NPC249408
0.6824 Remote Similarity NPC22918
0.6824 Remote Similarity NPC104129
0.6824 Remote Similarity NPC50464
0.6786 Remote Similarity NPC475037
0.6782 Remote Similarity NPC320552
0.6782 Remote Similarity NPC280390
0.6782 Remote Similarity NPC61201
0.6744 Remote Similarity NPC118078
0.6744 Remote Similarity NPC303451
0.6744 Remote Similarity NPC6414
0.6712 Remote Similarity NPC206601
0.6711 Remote Similarity NPC163812
0.6711 Remote Similarity NPC206823
0.6711 Remote Similarity NPC169085
0.6711 Remote Similarity NPC39266
0.6711 Remote Similarity NPC9763
0.6711 Remote Similarity NPC225748
0.6706 Remote Similarity NPC148534
0.6705 Remote Similarity NPC477927
0.6705 Remote Similarity NPC294293
0.6705 Remote Similarity NPC72817
0.6667 Remote Similarity NPC149018
0.6667 Remote Similarity NPC171484
0.6667 Remote Similarity NPC472197
0.6667 Remote Similarity NPC76486
0.6667 Remote Similarity NPC9447
0.6667 Remote Similarity NPC70756
0.6667 Remote Similarity NPC471879
0.6667 Remote Similarity NPC276298
0.6667 Remote Similarity NPC472199
0.6667 Remote Similarity NPC320240
0.6667 Remote Similarity NPC279575
0.6667 Remote Similarity NPC208473
0.6629 Remote Similarity NPC469543
0.6629 Remote Similarity NPC101051
0.6628 Remote Similarity NPC477748
0.6627 Remote Similarity NPC166279
0.6627 Remote Similarity NPC288471
0.6623 Remote Similarity NPC166250
0.662 Remote Similarity NPC268243
0.662 Remote Similarity NPC325773
0.6613 Remote Similarity NPC252918
0.6613 Remote Similarity NPC230789
0.6591 Remote Similarity NPC472195
0.6591 Remote Similarity NPC472196
0.6591 Remote Similarity NPC238090
0.6588 Remote Similarity NPC258501
0.6579 Remote Similarity NPC185419
0.6579 Remote Similarity NPC184550
0.6556 Remote Similarity NPC256230
0.6552 Remote Similarity NPC202886
0.6548 Remote Similarity NPC475034
0.6522 Remote Similarity NPC64348
0.6522 Remote Similarity NPC91497
0.6517 Remote Similarity NPC262312
0.6517 Remote Similarity NPC159698
0.6517 Remote Similarity NPC63897
0.6517 Remote Similarity NPC23454

  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 NPC147292 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
0.8167 Intermediate Similarity NPD893 Approved
0.8167 Intermediate Similarity NPD890 Clinical (unspecified phase)
0.8167 Intermediate Similarity NPD888 Phase 3
0.8167 Intermediate Similarity NPD892 Phase 3
0.8167 Intermediate Similarity NPD891 Phase 3
0.7833 Intermediate Similarity NPD904 Phase 3
0.7833 Intermediate Similarity NPD905 Approved
0.7705 Intermediate Similarity NPD2269 Approved
0.7581 Intermediate Similarity NPD887 Approved
0.7581 Intermediate Similarity NPD889 Approved
0.7581 Intermediate Similarity NPD894 Approved
0.7581 Intermediate Similarity NPD895 Approved
0.7576 Intermediate Similarity NPD6123 Approved
0.7188 Intermediate Similarity NPD7346 Approved
0.7 Intermediate Similarity NPD8998 Phase 2
0.7 Intermediate Similarity NPD9000 Phase 3
0.7 Intermediate Similarity NPD8993 Phase 1
0.7 Intermediate Similarity NPD8997 Approved
0.7 Intermediate Similarity NPD8999 Phase 3
0.697 Remote Similarity NPD2267 Suspended
0.6866 Remote Similarity NPD369 Approved
0.6774 Remote Similarity NPD8966 Approved
0.6774 Remote Similarity NPD8965 Approved
0.662 Remote Similarity NPD847 Phase 1
0.6515 Remote Similarity NPD9035 Clinical (unspecified phase)
0.6515 Remote Similarity NPD9036 Phase 3
0.65 Remote Similarity NPD8788 Approved
0.6494 Remote Similarity NPD3181 Approved
0.6267 Remote Similarity NPD896 Approved
0.6267 Remote Similarity NPD898 Approved
0.6267 Remote Similarity NPD897 Approved
0.622 Remote Similarity NPD7329 Approved
0.618 Remote Similarity NPD8522 Clinical (unspecified phase)
0.6129 Remote Similarity NPD9006 Approved
0.6081 Remote Similarity NPD1457 Discontinued
0.6026 Remote Similarity NPD7532 Clinical (unspecified phase)
0.5895 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5857 Remote Similarity NPD885 Approved
0.5857 Remote Similarity NPD884 Clinical (unspecified phase)
0.5825 Remote Similarity NPD6430 Approved
0.5825 Remote Similarity NPD6429 Approved
0.5824 Remote Similarity NPD46 Approved
0.5824 Remote Similarity NPD6698 Approved
0.5802 Remote Similarity NPD1810 Approved
0.5802 Remote Similarity NPD1811 Approved
0.5781 Remote Similarity NPD9218 Clinical (unspecified phase)
0.5781 Remote Similarity NPD9219 Approved
0.5743 Remote Similarity NPD6686 Approved
0.5692 Remote Similarity NPD8994 Approved
0.5652 Remote Similarity NPD9049 Discontinued
0.5652 Remote Similarity NPD9050 Approved
0.5644 Remote Similarity NPD6412 Phase 2
0.5619 Remote Similarity NPD8133 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