Structure

Physi-Chem Properties

Molecular Weight:  1076.58
Volume:  1033.064
LogP:  1.386
LogD:  1.714
LogS:  -3.733
# Rotatable Bonds:  11
TPSA:  346.06
# H-Bond Aceptor:  22
# H-Bond Donor:  13
# Rings:  10
# Heavy Atoms:  22

MedChem Properties

QED Drug-Likeness Score:  0.102
Synthetic Accessibility Score:  5.132
Fsp3:  1.0
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.313
MDCK Permeability:  6.465820479206741e-05
Pgp-inhibitor:  0.032
Pgp-substrate:  0.996
Human Intestinal Absorption (HIA):  0.997
20% Bioavailability (F20%):  0.031
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.064
Plasma Protein Binding (PPB):  54.40101623535156%
Volume Distribution (VD):  -0.025
Pgp-substrate:  13.75772476196289%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.952
CYP2C19-inhibitor:  0.0
CYP2C19-substrate:  0.323
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.002
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.033
CYP3A4-inhibitor:  0.075
CYP3A4-substrate:  0.006

ADMET: Excretion

Clearance (CL):  0.219
Half-life (T1/2):  0.818

ADMET: Toxicity

hERG Blockers:  0.291
Human Hepatotoxicity (H-HT):  0.209
Drug-inuced Liver Injury (DILI):  0.003
AMES Toxicity:  0.059
Rat Oral Acute Toxicity:  0.101
Maximum Recommended Daily Dose:  0.669
Skin Sensitization:  0.876
Carcinogencity:  0.023
Eye Corrosion:  0.003
Eye Irritation:  0.008
Respiratory Toxicity:  0.92

Download Data

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

  Natural Product: NPC267238

Natural Product ID:  NPC267238
Common Name*:   Ardisicrenoside A
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LTTSWSWZQNISIB-LLEYBADXSA-N
Standard InCHI:  InChI=1S/C53H88O22/c1-23-32(58)36(62)39(65)43(69-23)75-42-38(64)34(60)25(19-55)71-46(42)72-26-20-67-45(41(35(26)61)74-44-40(66)37(63)33(59)24(18-54)70-44)73-31-10-11-49(5)27(47(31,2)3)8-12-50(6)28(49)9-13-53-29-16-48(4,21-56)14-15-52(29,22-68-53)30(57)17-51(50,53)7/h23-46,54-66H,8-22H2,1-7H3/t23-,24+,25+,26-,27-,28+,29+,30+,31-,32-,33+,34+,35-,36+,37-,38-,39+,40+,41+,42+,43-,44-,45-,46-,48-,49-,50+,51-,52+,53-/m0/s1
SMILES:  C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H]([C@@H]([C@@H](CO)O[C@H]1O[C@H]1CO[C@H]([C@@H]([C@H]1O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O[C@H]1CC[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2CC[C@]24[C@@H]5C[C@](C)(CC[C@]5(CO4)[C@@H](C[C@@]32C)O)CO)C1(C)C)O)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL373378
PubChem CID:   10260582
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

*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
NPO3803 Ardisia japonica Species Primulaceae Eukaryota whole plants Sendai, Miyagi Prefecture, Japan 2000-Sep PMID[17243725]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. whole plant n.a. PMID[17243725]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. whole plant n.a. PMID[17397219]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. PMID[22940450]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3803 Ardisia japonica Species Primulaceae 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
NPT116 Cell Line HL-60 Homo sapiens IC50 > 100000.0 nM PMID[510048]
NPT81 Cell Line A549 Homo sapiens IC50 > 100000.0 nM PMID[510048]
NPT181 Cell Line Bel-7402 Homo sapiens IC50 > 100000000.0 nM PMID[510049]
NPT65 Cell Line HepG2 Homo sapiens IC50 > 100000000.0 nM PMID[510049]
NPT27 Others Unspecified IC50 = 14500.0 nM PMID[510048]
NPT27 Others Unspecified IC50 > 100000000.0 nM PMID[510049]

☑ 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 NPC267238 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 NPC77717
1.0 High Similarity NPC148593
1.0 High Similarity NPC471373
1.0 High Similarity NPC253611
0.9886 High Similarity NPC471424
0.9886 High Similarity NPC205129
0.9886 High Similarity NPC106701
0.9886 High Similarity NPC471425
0.9886 High Similarity NPC189575
0.9886 High Similarity NPC471429
0.9885 High Similarity NPC470623
0.9885 High Similarity NPC171741
0.9885 High Similarity NPC18724
0.9885 High Similarity NPC323231
0.9885 High Similarity NPC224003
0.956 High Similarity NPC209798
0.956 High Similarity NPC471374
0.956 High Similarity NPC471375
0.9457 High Similarity NPC471426
0.9457 High Similarity NPC471428
0.9457 High Similarity NPC471427
0.9457 High Similarity NPC51579
0.9121 High Similarity NPC305418
0.9022 High Similarity NPC477494
0.8925 High Similarity NPC139271
0.8925 High Similarity NPC304011
0.8901 High Similarity NPC210759
0.8901 High Similarity NPC307167
0.8901 High Similarity NPC229801
0.8889 High Similarity NPC131466
0.8878 High Similarity NPC126753
0.8878 High Similarity NPC475234
0.8878 High Similarity NPC40716
0.8878 High Similarity NPC138219
0.8878 High Similarity NPC475630
0.883 High Similarity NPC274200
0.883 High Similarity NPC476112
0.883 High Similarity NPC307534
0.8817 High Similarity NPC107962
0.8817 High Similarity NPC211354
0.8817 High Similarity NPC206003
0.8817 High Similarity NPC19400
0.8817 High Similarity NPC473610
0.8817 High Similarity NPC475351
0.8817 High Similarity NPC6295
0.8817 High Similarity NPC473727
0.8817 High Similarity NPC107188
0.8804 High Similarity NPC172838
0.8804 High Similarity NPC137004
0.8788 High Similarity NPC231566
0.8788 High Similarity NPC262567
0.8788 High Similarity NPC471626
0.8788 High Similarity NPC207693
0.8788 High Similarity NPC473688
0.8776 High Similarity NPC184805
0.8776 High Similarity NPC119628
0.8776 High Similarity NPC273189
0.8776 High Similarity NPC158367
0.8776 High Similarity NPC158051
0.8737 High Similarity NPC473518
0.8723 High Similarity NPC121453
0.8723 High Similarity NPC473601
0.8723 High Similarity NPC232037
0.8723 High Similarity NPC30856
0.8723 High Similarity NPC475625
0.8723 High Similarity NPC103616
0.8723 High Similarity NPC470864
0.8723 High Similarity NPC284104
0.8723 High Similarity NPC97700
0.8723 High Similarity NPC116756
0.8723 High Similarity NPC160426
0.8723 High Similarity NPC287483
0.8723 High Similarity NPC128572
0.8723 High Similarity NPC195297
0.8723 High Similarity NPC98018
0.8723 High Similarity NPC470863
0.8723 High Similarity NPC475643
0.8723 High Similarity NPC470865
0.8723 High Similarity NPC132080
0.8723 High Similarity NPC184617
0.8723 High Similarity NPC84111
0.8723 High Similarity NPC470866
0.871 High Similarity NPC291547
0.871 High Similarity NPC253268
0.871 High Similarity NPC312678
0.871 High Similarity NPC264101
0.871 High Similarity NPC174024
0.871 High Similarity NPC291203
0.871 High Similarity NPC475436
0.871 High Similarity NPC252253
0.871 High Similarity NPC179859
0.871 High Similarity NPC473851
0.871 High Similarity NPC471464
0.871 High Similarity NPC217205
0.871 High Similarity NPC45959
0.871 High Similarity NPC131693
0.87 High Similarity NPC22709
0.8687 High Similarity NPC471430
0.8681 High Similarity NPC82955
0.8673 High Similarity NPC267637
0.8667 High Similarity NPC43912
0.8667 High Similarity NPC140446
0.8632 High Similarity NPC477222
0.8632 High Similarity NPC51520
0.8632 High Similarity NPC303069
0.8632 High Similarity NPC470861
0.8632 High Similarity NPC470862
0.8632 High Similarity NPC115165
0.8632 High Similarity NPC83137
0.8632 High Similarity NPC232611
0.8632 High Similarity NPC477223
0.8617 High Similarity NPC474399
0.8614 High Similarity NPC471431
0.8602 High Similarity NPC144790
0.8602 High Similarity NPC234352
0.8602 High Similarity NPC88962
0.8602 High Similarity NPC177834
0.8602 High Similarity NPC477547
0.8602 High Similarity NPC48339
0.8602 High Similarity NPC250393
0.8602 High Similarity NPC141769
0.8602 High Similarity NPC477451
0.8602 High Similarity NPC149400
0.8602 High Similarity NPC249204
0.8602 High Similarity NPC325828
0.8602 High Similarity NPC297348
0.8587 High Similarity NPC65550
0.8542 High Similarity NPC291548
0.8526 High Similarity NPC142264
0.8526 High Similarity NPC476510
0.8526 High Similarity NPC237071
0.8526 High Similarity NPC238796
0.8526 High Similarity NPC203434
0.8511 High Similarity NPC222731
0.8511 High Similarity NPC309866
0.8511 High Similarity NPC473774
0.8511 High Similarity NPC24960
0.8511 High Similarity NPC294686
0.8495 Intermediate Similarity NPC473830
0.8495 Intermediate Similarity NPC204881
0.8469 Intermediate Similarity NPC80640
0.8447 Intermediate Similarity NPC157571
0.8444 Intermediate Similarity NPC290612
0.8438 Intermediate Similarity NPC233649
0.8438 Intermediate Similarity NPC470591
0.8438 Intermediate Similarity NPC470028
0.8431 Intermediate Similarity NPC470622
0.8431 Intermediate Similarity NPC66513
0.8427 Intermediate Similarity NPC241959
0.8421 Intermediate Similarity NPC92196
0.8421 Intermediate Similarity NPC94582
0.8421 Intermediate Similarity NPC57964
0.8404 Intermediate Similarity NPC473726
0.8404 Intermediate Similarity NPC311246
0.8404 Intermediate Similarity NPC167644
0.8387 Intermediate Similarity NPC473542
0.8387 Intermediate Similarity NPC279329
0.837 Intermediate Similarity NPC281004
0.8367 Intermediate Similarity NPC475574
0.8352 Intermediate Similarity NPC471411
0.8352 Intermediate Similarity NPC471410
0.8333 Intermediate Similarity NPC87393
0.8316 Intermediate Similarity NPC3538
0.8316 Intermediate Similarity NPC175
0.8316 Intermediate Similarity NPC477224
0.8316 Intermediate Similarity NPC113500
0.83 Intermediate Similarity NPC476360
0.83 Intermediate Similarity NPC476361
0.8298 Intermediate Similarity NPC293609
0.8298 Intermediate Similarity NPC36372
0.8298 Intermediate Similarity NPC149966
0.8298 Intermediate Similarity NPC5632
0.8286 Intermediate Similarity NPC477465
0.828 Intermediate Similarity NPC102725
0.828 Intermediate Similarity NPC473472
0.8276 Intermediate Similarity NPC477577
0.8276 Intermediate Similarity NPC272841
0.8276 Intermediate Similarity NPC177343
0.8269 Intermediate Similarity NPC476305
0.8265 Intermediate Similarity NPC80417
0.8247 Intermediate Similarity NPC475207
0.8247 Intermediate Similarity NPC210157
0.8229 Intermediate Similarity NPC473065
0.8229 Intermediate Similarity NPC473067
0.8229 Intermediate Similarity NPC473064
0.8211 Intermediate Similarity NPC277774
0.82 Intermediate Similarity NPC123796
0.8191 Intermediate Similarity NPC223143
0.8182 Intermediate Similarity NPC108227
0.8182 Intermediate Similarity NPC476512
0.8182 Intermediate Similarity NPC476839
0.8182 Intermediate Similarity NPC472081
0.8182 Intermediate Similarity NPC476838
0.8173 Intermediate Similarity NPC157474
0.8173 Intermediate Similarity NPC110494
0.8163 Intermediate Similarity NPC473638
0.8163 Intermediate Similarity NPC473616
0.8144 Intermediate Similarity NPC296936
0.8137 Intermediate Similarity NPC14946
0.8137 Intermediate Similarity NPC208650

  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 NPC267238 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
0.8602 High Similarity NPD8171 Discontinued
0.7767 Intermediate Similarity NPD8170 Clinical (unspecified phase)
0.7364 Intermediate Similarity NPD8133 Approved
0.7312 Intermediate Similarity NPD6928 Phase 2
0.7222 Intermediate Similarity NPD1810 Approved
0.7222 Intermediate Similarity NPD1811 Approved
0.6983 Remote Similarity NPD8294 Approved
0.6983 Remote Similarity NPD8377 Approved
0.6923 Remote Similarity NPD8379 Approved
0.6923 Remote Similarity NPD8296 Approved
0.6923 Remote Similarity NPD8378 Approved
0.6923 Remote Similarity NPD8380 Approved
0.6923 Remote Similarity NPD8335 Approved
0.6889 Remote Similarity NPD2687 Approved
0.6889 Remote Similarity NPD2686 Approved
0.6889 Remote Similarity NPD2254 Approved
0.687 Remote Similarity NPD8295 Clinical (unspecified phase)
0.6847 Remote Similarity NPD8132 Clinical (unspecified phase)
0.678 Remote Similarity NPD8033 Approved
0.6778 Remote Similarity NPD4267 Clinical (unspecified phase)
0.6735 Remote Similarity NPD3670 Clinical (unspecified phase)
0.6735 Remote Similarity NPD3669 Approved
0.6703 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6667 Remote Similarity NPD7327 Approved
0.6667 Remote Similarity NPD8328 Phase 3
0.6667 Remote Similarity NPD7328 Approved
0.661 Remote Similarity NPD7516 Approved
0.6509 Remote Similarity NPD7991 Discontinued
0.6437 Remote Similarity NPD6123 Approved
0.6404 Remote Similarity NPD371 Approved
0.623 Remote Similarity NPD7503 Approved
0.6228 Remote Similarity NPD6412 Phase 2
0.6218 Remote Similarity NPD6940 Discontinued
0.6202 Remote Similarity NPD8450 Suspended
0.6174 Remote Similarity NPD8174 Phase 2
0.616 Remote Similarity NPD7507 Approved
0.6124 Remote Similarity NPD8449 Approved
0.6098 Remote Similarity NPD8517 Approved
0.6098 Remote Similarity NPD8515 Approved
0.6098 Remote Similarity NPD8516 Approved
0.6061 Remote Similarity NPD6114 Approved
0.6061 Remote Similarity NPD6118 Approved
0.6061 Remote Similarity NPD6115 Approved
0.6061 Remote Similarity NPD6697 Approved
0.604 Remote Similarity NPD1779 Approved
0.604 Remote Similarity NPD1780 Approved
0.6034 Remote Similarity NPD6686 Approved
0.6016 Remote Similarity NPD7319 Approved
0.6 Remote Similarity NPD7645 Phase 2
0.5968 Remote Similarity NPD8513 Phase 3
0.596 Remote Similarity NPD6116 Phase 1
0.5938 Remote Similarity NPD7736 Approved
0.5897 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5859 Remote Similarity NPD6117 Approved
0.5833 Remote Similarity NPD4787 Phase 1
0.5794 Remote Similarity NPD6370 Approved
0.5784 Remote Similarity NPD7525 Registered
0.578 Remote Similarity NPD8035 Phase 2
0.578 Remote Similarity NPD8034 Phase 2
0.5758 Remote Similarity NPD3703 Phase 2
0.575 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5747 Remote Similarity NPD7346 Approved
0.5736 Remote Similarity NPD8293 Discontinued
0.5714 Remote Similarity NPD4061 Clinical (unspecified phase)
0.5657 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5635 Remote Similarity NPD6054 Approved
0.5635 Remote Similarity NPD6059 Approved
0.5632 Remote Similarity NPD890 Clinical (unspecified phase)
0.5632 Remote Similarity NPD889 Approved
0.5632 Remote Similarity NPD892 Phase 3
0.5632 Remote Similarity NPD895 Approved
0.5632 Remote Similarity NPD891 Phase 3
0.5632 Remote Similarity NPD887 Approved
0.5632 Remote Similarity NPD893 Approved
0.5632 Remote Similarity NPD894 Approved
0.5632 Remote Similarity NPD888 Phase 3
0.5618 Remote Similarity NPD2267 Suspended
0.5612 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5612 Remote Similarity NPD4808 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