Structure

Physi-Chem Properties

Molecular Weight:  510.21
Volume:  508.0
LogP:  1.846
LogD:  1.148
LogS:  -2.552
# Rotatable Bonds:  13
TPSA:  151.73
# H-Bond Aceptor:  11
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.289
Synthetic Accessibility Score:  4.338
Fsp3:  0.56
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.836
MDCK Permeability:  8.64034445839934e-05
Pgp-inhibitor:  1.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.91
20% Bioavailability (F20%):  0.87
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.095
Plasma Protein Binding (PPB):  49.33983612060547%
Volume Distribution (VD):  1.833
Pgp-substrate:  14.451789855957031%

ADMET: Metabolism

CYP1A2-inhibitor:  0.519
CYP1A2-substrate:  0.086
CYP2C19-inhibitor:  0.405
CYP2C19-substrate:  0.115
CYP2C9-inhibitor:  0.832
CYP2C9-substrate:  0.048
CYP2D6-inhibitor:  0.958
CYP2D6-substrate:  0.029
CYP3A4-inhibitor:  0.882
CYP3A4-substrate:  0.196

ADMET: Excretion

Clearance (CL):  5.846
Half-life (T1/2):  0.942

ADMET: Toxicity

hERG Blockers:  0.044
Human Hepatotoxicity (H-HT):  0.985
Drug-inuced Liver Injury (DILI):  0.859
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.01
Maximum Recommended Daily Dose:  0.044
Skin Sensitization:  0.605
Carcinogencity:  0.024
Eye Corrosion:  0.035
Eye Irritation:  0.252
Respiratory Toxicity:  0.167

Download Data

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

  Natural Product: NPC477313

Natural Product ID:  NPC477313
Common Name*:   1-O,6-O-Diacetyl-2-O,4-O,5-O-trisangeloyl-L-chiro-inositol
IUPAC Name:   [(1S,2S,3R,4S,5R,6S)-2,3-diacetyloxy-6-hydroxy-4,5-bis[[(Z)-2-methylbut-2-enoyl]oxy]cyclohexyl] (Z)-2-methylbut-2-enoate
Synonyms:  
Standard InCHIKey:  DSYJAAFDCLPHRE-HKWJVIHUSA-N
Standard InCHI:  InChI=1S/C25H34O11/c1-9-12(4)23(29)34-18-17(28)19(35-24(30)13(5)10-2)21(36-25(31)14(6)11-3)22(33-16(8)27)20(18)32-15(7)26/h9-11,17-22,28H,1-8H3/b12-9-,13-10-,14-11-/t17-,18-,19+,20-,21-,22+/m0/s1
SMILES:  C/C=C(/C)\C(=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H]([C@H]1OC(=O)C)OC(=O)C)OC(=O)/C(=C\C)/C)OC(=O)/C(=C\C)/C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   122195885
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0002995] Pentacarboxylic acids and derivatives

*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
NPO30455 Inula cappa Species Asteraceae Eukaryota Whole Plant Yulin County, Guangxi Province, China 2012-SEP PMID[26444098]

☑ 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
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 7100 nM PMID[26444098]

☑ 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 NPC477313 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 NPC477312
1.0 High Similarity NPC477308
1.0 High Similarity NPC477305
1.0 High Similarity NPC477316
1.0 High Similarity NPC477309
1.0 High Similarity NPC477304
1.0 High Similarity NPC477315
0.9855 High Similarity NPC477306
0.9853 High Similarity NPC477303
0.9853 High Similarity NPC477311
0.9444 High Similarity NPC477314
0.7727 Intermediate Similarity NPC469583
0.764 Intermediate Similarity NPC472997
0.764 Intermediate Similarity NPC472996
0.764 Intermediate Similarity NPC472995
0.7625 Intermediate Similarity NPC180725
0.7595 Intermediate Similarity NPC475711
0.7595 Intermediate Similarity NPC474026
0.759 Intermediate Similarity NPC288471
0.7556 Intermediate Similarity NPC472998
0.7531 Intermediate Similarity NPC133226
0.7531 Intermediate Similarity NPC470147
0.7529 Intermediate Similarity NPC118077
0.7529 Intermediate Similarity NPC475186
0.75 Intermediate Similarity NPC470124
0.75 Intermediate Similarity NPC248775
0.7439 Intermediate Similarity NPC469469
0.7407 Intermediate Similarity NPC470148
0.7407 Intermediate Similarity NPC470149
0.7381 Intermediate Similarity NPC475035
0.7381 Intermediate Similarity NPC266718
0.7356 Intermediate Similarity NPC285588
0.7349 Intermediate Similarity NPC251026
0.7326 Intermediate Similarity NPC475037
0.7317 Intermediate Similarity NPC127295
0.7317 Intermediate Similarity NPC163362
0.7294 Intermediate Similarity NPC329615
0.7294 Intermediate Similarity NPC471567
0.7294 Intermediate Similarity NPC329838
0.7294 Intermediate Similarity NPC477014
0.7294 Intermediate Similarity NPC120398
0.7294 Intermediate Similarity NPC477013
0.7294 Intermediate Similarity NPC475034
0.7262 Intermediate Similarity NPC142111
0.7262 Intermediate Similarity NPC473315
0.7241 Intermediate Similarity NPC89001
0.7241 Intermediate Similarity NPC20339
0.7241 Intermediate Similarity NPC473905
0.7241 Intermediate Similarity NPC40376
0.7241 Intermediate Similarity NPC320458
0.7241 Intermediate Similarity NPC233551
0.7241 Intermediate Similarity NPC21208
0.7241 Intermediate Similarity NPC280621
0.7241 Intermediate Similarity NPC48338
0.7209 Intermediate Similarity NPC477015
0.7209 Intermediate Similarity NPC47937
0.7191 Intermediate Similarity NPC477349
0.7191 Intermediate Similarity NPC110072
0.7176 Intermediate Similarity NPC156804
0.7176 Intermediate Similarity NPC163093
0.7176 Intermediate Similarity NPC473308
0.7159 Intermediate Similarity NPC477016
0.7159 Intermediate Similarity NPC477017
0.7126 Intermediate Similarity NPC178215
0.7126 Intermediate Similarity NPC20533
0.7126 Intermediate Similarity NPC476583
0.7126 Intermediate Similarity NPC258068
0.7125 Intermediate Similarity NPC327041
0.7125 Intermediate Similarity NPC285840
0.7111 Intermediate Similarity NPC472196
0.7111 Intermediate Similarity NPC472195
0.7111 Intermediate Similarity NPC238090
0.7093 Intermediate Similarity NPC322529
0.7093 Intermediate Similarity NPC182383
0.7089 Intermediate Similarity NPC327383
0.7089 Intermediate Similarity NPC185186
0.7079 Intermediate Similarity NPC177668
0.7079 Intermediate Similarity NPC239517
0.7079 Intermediate Similarity NPC118078
0.7073 Intermediate Similarity NPC317263
0.7051 Intermediate Similarity NPC476012
0.7045 Intermediate Similarity NPC470137
0.7033 Intermediate Similarity NPC44682
0.7033 Intermediate Similarity NPC477348
0.7033 Intermediate Similarity NPC163409
0.7033 Intermediate Similarity NPC477345
0.7033 Intermediate Similarity NPC238264
0.7033 Intermediate Similarity NPC159698
0.7011 Intermediate Similarity NPC25703
0.7011 Intermediate Similarity NPC107717
0.7011 Intermediate Similarity NPC293136
0.7011 Intermediate Similarity NPC134865
0.7011 Intermediate Similarity NPC142117
0.7011 Intermediate Similarity NPC282815
0.7011 Intermediate Similarity NPC473840
0.7011 Intermediate Similarity NPC132940
0.7011 Intermediate Similarity NPC232555
0.7011 Intermediate Similarity NPC171174
0.7011 Intermediate Similarity NPC241360
0.7011 Intermediate Similarity NPC62118
0.7011 Intermediate Similarity NPC219652
0.7011 Intermediate Similarity NPC114694
0.7011 Intermediate Similarity NPC103523
0.7011 Intermediate Similarity NPC208473
0.7011 Intermediate Similarity NPC240695
0.7011 Intermediate Similarity NPC475581
0.7011 Intermediate Similarity NPC231096
0.7 Intermediate Similarity NPC477749
0.7 Intermediate Similarity NPC107654
0.6988 Remote Similarity NPC1180
0.6966 Remote Similarity NPC473504
0.6966 Remote Similarity NPC280612
0.6966 Remote Similarity NPC40066
0.6966 Remote Similarity NPC93794
0.6966 Remote Similarity NPC42598
0.6966 Remote Similarity NPC81778
0.6966 Remote Similarity NPC477011
0.6966 Remote Similarity NPC91067
0.6966 Remote Similarity NPC318963
0.6966 Remote Similarity NPC133450
0.6966 Remote Similarity NPC20621
0.6962 Remote Similarity NPC475762
0.6951 Remote Similarity NPC477203
0.6941 Remote Similarity NPC180363
0.6941 Remote Similarity NPC473529
0.6941 Remote Similarity NPC473712
0.6941 Remote Similarity NPC131002
0.6941 Remote Similarity NPC473780
0.6941 Remote Similarity NPC11332
0.6941 Remote Similarity NPC73310
0.6941 Remote Similarity NPC65930
0.6941 Remote Similarity NPC94875
0.6941 Remote Similarity NPC475159
0.6941 Remote Similarity NPC329829
0.6941 Remote Similarity NPC145914
0.6932 Remote Similarity NPC473995
0.6897 Remote Similarity NPC110710
0.6897 Remote Similarity NPC292809
0.6897 Remote Similarity NPC223871
0.6897 Remote Similarity NPC473478
0.6897 Remote Similarity NPC473669
0.6897 Remote Similarity NPC283085
0.6897 Remote Similarity NPC231009
0.6897 Remote Similarity NPC66346
0.6897 Remote Similarity NPC473671
0.6897 Remote Similarity NPC103284
0.6897 Remote Similarity NPC475268
0.6897 Remote Similarity NPC477018
0.6897 Remote Similarity NPC470400
0.6897 Remote Similarity NPC1083
0.6897 Remote Similarity NPC286338
0.6897 Remote Similarity NPC235809
0.6897 Remote Similarity NPC202055
0.6897 Remote Similarity NPC39279
0.6897 Remote Similarity NPC39167
0.6897 Remote Similarity NPC132496
0.6897 Remote Similarity NPC473156
0.6897 Remote Similarity NPC100921
0.6897 Remote Similarity NPC77871
0.6897 Remote Similarity NPC25764
0.6897 Remote Similarity NPC319036
0.6897 Remote Similarity NPC473651
0.6897 Remote Similarity NPC9678
0.6897 Remote Similarity NPC82795
0.6897 Remote Similarity NPC107986
0.6889 Remote Similarity NPC473904
0.6889 Remote Similarity NPC6414
0.6889 Remote Similarity NPC3952
0.6889 Remote Similarity NPC473311
0.6889 Remote Similarity NPC303451
0.6882 Remote Similarity NPC475164
0.6882 Remote Similarity NPC475525
0.6882 Remote Similarity NPC475375
0.6882 Remote Similarity NPC476066
0.6882 Remote Similarity NPC473605
0.6882 Remote Similarity NPC475241
0.6882 Remote Similarity NPC473765
0.6882 Remote Similarity NPC475540
0.6882 Remote Similarity NPC475593
0.6875 Remote Similarity NPC329914
0.686 Remote Similarity NPC253801
0.686 Remote Similarity NPC144415
0.6854 Remote Similarity NPC169511
0.6854 Remote Similarity NPC100454
0.6854 Remote Similarity NPC133730
0.6854 Remote Similarity NPC39754
0.6854 Remote Similarity NPC171135
0.6854 Remote Similarity NPC234077
0.6854 Remote Similarity NPC261952
0.6854 Remote Similarity NPC287164
0.6854 Remote Similarity NPC320569
0.6854 Remote Similarity NPC151403
0.6854 Remote Similarity NPC242364
0.6854 Remote Similarity NPC172821
0.6854 Remote Similarity NPC61257
0.6854 Remote Similarity NPC191929
0.6854 Remote Similarity NPC81045
0.6854 Remote Similarity NPC274446
0.6848 Remote Similarity NPC294293
0.6848 Remote Similarity NPC256368

  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 NPC477313 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
0.7079 Intermediate Similarity NPD7838 Discovery
0.7079 Intermediate Similarity NPD6698 Approved
0.7079 Intermediate Similarity NPD46 Approved
0.6947 Remote Similarity NPD5344 Discontinued
0.6495 Remote Similarity NPD6648 Approved
0.6392 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6373 Remote Similarity NPD6686 Approved
0.622 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6111 Remote Similarity NPD6110 Phase 1
0.6105 Remote Similarity NPD7983 Approved
0.6029 Remote Similarity NPD9218 Clinical (unspecified phase)
0.6029 Remote Similarity NPD9219 Approved
0.5962 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5946 Remote Similarity NPD7516 Approved
0.59 Remote Similarity NPD4225 Approved
0.5856 Remote Similarity NPD7327 Approved
0.5856 Remote Similarity NPD7328 Approved
0.5849 Remote Similarity NPD4061 Clinical (unspecified phase)
0.5794 Remote Similarity NPD6371 Approved
0.5743 Remote Similarity NPD7638 Approved
0.5733 Remote Similarity NPD3728 Approved
0.5733 Remote Similarity NPD3730 Approved
0.5699 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5686 Remote Similarity NPD7640 Approved
0.5686 Remote Similarity NPD7639 Approved
0.5676 Remote Similarity NPD2269 Approved
0.5663 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5648 Remote Similarity NPD5955 Clinical (unspecified phase)
0.5641 Remote Similarity NPD6109 Phase 1
0.5612 Remote Similarity NPD7637 Suspended
0.561 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5607 Remote Similarity NPD5345 Clinical (unspecified phase)

  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