Structure

Physi-Chem Properties

Molecular Weight:  958.55
Volume:  937.276
LogP:  2.666
LogD:  2.766
LogS:  -4.744
# Rotatable Bonds:  10
TPSA:  265.14
# H-Bond Aceptor:  18
# H-Bond Donor:  9
# Rings:  9
# Heavy Atoms:  18

MedChem Properties

QED Drug-Likeness Score:  0.11
Synthetic Accessibility Score:  7.75
Fsp3:  1.0
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.723
MDCK Permeability:  4.3875534174731e-05
Pgp-inhibitor:  0.288
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.906
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.759

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.005
Plasma Protein Binding (PPB):  64.23007202148438%
Volume Distribution (VD):  0.125
Pgp-substrate:  13.005743980407715%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.981
CYP2C19-inhibitor:  0.001
CYP2C19-substrate:  0.63
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.003
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.057
CYP3A4-inhibitor:  0.092
CYP3A4-substrate:  0.028

ADMET: Excretion

Clearance (CL):  0.505
Half-life (T1/2):  0.727

ADMET: Toxicity

hERG Blockers:  0.232
Human Hepatotoxicity (H-HT):  0.231
Drug-inuced Liver Injury (DILI):  0.004
AMES Toxicity:  0.063
Rat Oral Acute Toxicity:  0.125
Maximum Recommended Daily Dose:  0.575
Skin Sensitization:  0.878
Carcinogencity:  0.027
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.977

Download Data

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

  Natural Product: NPC470623

Natural Product ID:  NPC470623
Common Name*:   ISOGVTOTWKVAFW-SFJUKZGFSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ISOGVTOTWKVAFW-SFJUKZGFSA-N
Standard InCHI:  InChI=1S/C49H82O18/c1-23-31(52)34(55)37(58)40(63-23)67-38-35(56)32(53)24(20-50)64-41(38)65-25-21-61-39(36(57)33(25)54)66-30-12-13-45(5)26(43(30,2)3)10-14-46(6)27(45)11-15-49-28-18-44(4,42(59-8)60-9)16-17-48(28,22-62-49)29(51)19-47(46,49)7/h23-42,50-58H,10-22H2,1-9H3/t23-,24+,25-,26-,27+,28+,29+,30-,31-,32+,33-,34+,35-,36+,37+,38+,39-,40-,41-,44-,45-,46+,47-,48+,49-/m0/s1
SMILES:  CC1C(C(C(C(O1)OC2C(C(C(OC2OC3COC(C(C3O)O)OC4CCC5(C(C4(C)C)CCC6(C5CCC78C6(CC(C9(C7CC(CC9)(C)C(OC)OC)CO8)O)C)C)C)CO)O)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2088615
PubChem CID:   70684876
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 n.a. whole plant n.a. PMID[17243725]
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[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
NPT181 Cell Line Bel-7402 Homo sapiens IC50 > 100000000.0 nM PMID[494445]
NPT65 Cell Line HepG2 Homo sapiens IC50 > 100000000.0 nM PMID[494445]
NPT27 Others Unspecified IC50 > 100000000.0 nM PMID[494445]

☑ 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 NPC470623 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 NPC18724
1.0 High Similarity NPC323231
1.0 High Similarity NPC224003
1.0 High Similarity NPC171741
0.9885 High Similarity NPC148593
0.9885 High Similarity NPC471373
0.9885 High Similarity NPC77717
0.9885 High Similarity NPC267238
0.9885 High Similarity NPC253611
0.9773 High Similarity NPC471425
0.9773 High Similarity NPC471429
0.9773 High Similarity NPC106701
0.9773 High Similarity NPC205129
0.9773 High Similarity NPC189575
0.9773 High Similarity NPC471424
0.9451 High Similarity NPC471375
0.9451 High Similarity NPC209798
0.9451 High Similarity NPC471374
0.9348 High Similarity NPC471427
0.9348 High Similarity NPC471428
0.9348 High Similarity NPC51579
0.9348 High Similarity NPC471426
0.9222 High Similarity NPC305418
0.9022 High Similarity NPC304011
0.9022 High Similarity NPC139271
0.9 High Similarity NPC307167
0.9 High Similarity NPC210759
0.9 High Similarity NPC229801
0.8989 High Similarity NPC131466
0.8913 High Similarity NPC477494
0.8901 High Similarity NPC137004
0.8901 High Similarity NPC172838
0.8866 High Similarity NPC158367
0.8866 High Similarity NPC158051
0.8866 High Similarity NPC119628
0.8817 High Similarity NPC121453
0.8804 High Similarity NPC174024
0.8804 High Similarity NPC475436
0.8804 High Similarity NPC45959
0.8804 High Similarity NPC473851
0.8804 High Similarity NPC131693
0.8804 High Similarity NPC252253
0.8804 High Similarity NPC291203
0.8804 High Similarity NPC179859
0.8804 High Similarity NPC217205
0.8804 High Similarity NPC312678
0.8804 High Similarity NPC253268
0.8804 High Similarity NPC291547
0.8778 High Similarity NPC82955
0.8776 High Similarity NPC138219
0.8776 High Similarity NPC126753
0.8776 High Similarity NPC40716
0.8776 High Similarity NPC475234
0.8776 High Similarity NPC475630
0.8764 High Similarity NPC43912
0.8764 High Similarity NPC140446
0.8763 High Similarity NPC267637
0.8723 High Similarity NPC476112
0.8723 High Similarity NPC307534
0.8723 High Similarity NPC477222
0.8723 High Similarity NPC477223
0.8723 High Similarity NPC274200
0.871 High Similarity NPC475351
0.871 High Similarity NPC474399
0.871 High Similarity NPC19400
0.871 High Similarity NPC107962
0.871 High Similarity NPC6295
0.871 High Similarity NPC211354
0.871 High Similarity NPC206003
0.871 High Similarity NPC107188
0.871 High Similarity NPC473727
0.871 High Similarity NPC473610
0.8696 High Similarity NPC48339
0.8696 High Similarity NPC149400
0.8696 High Similarity NPC234352
0.8696 High Similarity NPC88962
0.8696 High Similarity NPC325828
0.8696 High Similarity NPC477451
0.8696 High Similarity NPC477547
0.8696 High Similarity NPC249204
0.8696 High Similarity NPC297348
0.8696 High Similarity NPC144790
0.8696 High Similarity NPC250393
0.8696 High Similarity NPC177834
0.8696 High Similarity NPC141769
0.8687 High Similarity NPC231566
0.8687 High Similarity NPC262567
0.8687 High Similarity NPC471626
0.8687 High Similarity NPC473688
0.8687 High Similarity NPC207693
0.8681 High Similarity NPC65550
0.8673 High Similarity NPC273189
0.8673 High Similarity NPC184805
0.8632 High Similarity NPC473518
0.8617 High Similarity NPC103616
0.8617 High Similarity NPC203434
0.8617 High Similarity NPC475643
0.8617 High Similarity NPC232037
0.8617 High Similarity NPC476510
0.8617 High Similarity NPC98018
0.8617 High Similarity NPC97700
0.8617 High Similarity NPC470863
0.8617 High Similarity NPC473601
0.8617 High Similarity NPC287483
0.8617 High Similarity NPC475625
0.8617 High Similarity NPC142264
0.8617 High Similarity NPC128572
0.8617 High Similarity NPC284104
0.8617 High Similarity NPC470864
0.8617 High Similarity NPC132080
0.8617 High Similarity NPC238796
0.8617 High Similarity NPC160426
0.8617 High Similarity NPC237071
0.8617 High Similarity NPC116756
0.8617 High Similarity NPC184617
0.8617 High Similarity NPC195297
0.8617 High Similarity NPC30856
0.8617 High Similarity NPC470865
0.8617 High Similarity NPC84111
0.8617 High Similarity NPC470866
0.8602 High Similarity NPC294686
0.8602 High Similarity NPC24960
0.8602 High Similarity NPC309866
0.8602 High Similarity NPC264101
0.8602 High Similarity NPC222731
0.8602 High Similarity NPC471464
0.8602 High Similarity NPC473774
0.86 High Similarity NPC22709
0.8587 High Similarity NPC473830
0.8587 High Similarity NPC204881
0.8586 High Similarity NPC471430
0.8557 High Similarity NPC80640
0.8539 High Similarity NPC290612
0.8526 High Similarity NPC470028
0.8526 High Similarity NPC470591
0.8526 High Similarity NPC83137
0.8526 High Similarity NPC470862
0.8526 High Similarity NPC303069
0.8526 High Similarity NPC232611
0.8526 High Similarity NPC51520
0.8526 High Similarity NPC470861
0.8526 High Similarity NPC233649
0.8526 High Similarity NPC115165
0.8523 High Similarity NPC241959
0.8515 High Similarity NPC471431
0.8511 High Similarity NPC57964
0.8511 High Similarity NPC92196
0.8511 High Similarity NPC94582
0.8495 Intermediate Similarity NPC167644
0.8495 Intermediate Similarity NPC311246
0.8495 Intermediate Similarity NPC473726
0.8478 Intermediate Similarity NPC279329
0.8478 Intermediate Similarity NPC473542
0.8462 Intermediate Similarity NPC281004
0.8454 Intermediate Similarity NPC475574
0.8444 Intermediate Similarity NPC471410
0.8444 Intermediate Similarity NPC471411
0.8438 Intermediate Similarity NPC291548
0.8416 Intermediate Similarity NPC87393
0.8404 Intermediate Similarity NPC113500
0.8404 Intermediate Similarity NPC3538
0.8404 Intermediate Similarity NPC175
0.8404 Intermediate Similarity NPC477224
0.8387 Intermediate Similarity NPC293609
0.8387 Intermediate Similarity NPC149966
0.8387 Intermediate Similarity NPC5632
0.8387 Intermediate Similarity NPC36372
0.8372 Intermediate Similarity NPC177343
0.8372 Intermediate Similarity NPC272841
0.8372 Intermediate Similarity NPC477577
0.837 Intermediate Similarity NPC102725
0.837 Intermediate Similarity NPC473472
0.8351 Intermediate Similarity NPC80417
0.835 Intermediate Similarity NPC157571
0.8333 Intermediate Similarity NPC475207
0.8333 Intermediate Similarity NPC210157
0.8333 Intermediate Similarity NPC66513
0.8333 Intermediate Similarity NPC470622
0.8316 Intermediate Similarity NPC473067
0.8316 Intermediate Similarity NPC473065
0.8316 Intermediate Similarity NPC473064
0.8298 Intermediate Similarity NPC277774
0.828 Intermediate Similarity NPC223143
0.8265 Intermediate Similarity NPC472081
0.8265 Intermediate Similarity NPC476839
0.8265 Intermediate Similarity NPC108227
0.8265 Intermediate Similarity NPC476838
0.8265 Intermediate Similarity NPC476512
0.8252 Intermediate Similarity NPC157474
0.8252 Intermediate Similarity NPC110494
0.8247 Intermediate Similarity NPC473638
0.8247 Intermediate Similarity NPC473616
0.8229 Intermediate Similarity NPC296936
0.8211 Intermediate Similarity NPC151214
0.8211 Intermediate Similarity NPC191915
0.8211 Intermediate Similarity NPC473503
0.82 Intermediate Similarity NPC469827
0.82 Intermediate Similarity NPC476360
0.82 Intermediate Similarity NPC476361
0.8191 Intermediate Similarity NPC476668

  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 NPC470623 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
0.8696 High Similarity NPD8171 Discontinued
0.7843 Intermediate Similarity NPD8170 Clinical (unspecified phase)
0.7431 Intermediate Similarity NPD8133 Approved
0.7391 Intermediate Similarity NPD6928 Phase 2
0.7303 Intermediate Similarity NPD1810 Approved
0.7303 Intermediate Similarity NPD1811 Approved
0.7043 Intermediate Similarity NPD8294 Approved
0.7043 Intermediate Similarity NPD8377 Approved
0.6983 Remote Similarity NPD8378 Approved
0.6983 Remote Similarity NPD8296 Approved
0.6983 Remote Similarity NPD8380 Approved
0.6983 Remote Similarity NPD8335 Approved
0.6983 Remote Similarity NPD8379 Approved
0.6966 Remote Similarity NPD2686 Approved
0.6966 Remote Similarity NPD2687 Approved
0.6966 Remote Similarity NPD2254 Approved
0.693 Remote Similarity NPD8295 Clinical (unspecified phase)
0.6909 Remote Similarity NPD8132 Clinical (unspecified phase)
0.6854 Remote Similarity NPD4267 Clinical (unspecified phase)
0.6838 Remote Similarity NPD8033 Approved
0.6804 Remote Similarity NPD3670 Clinical (unspecified phase)
0.6804 Remote Similarity NPD3669 Approved
0.6778 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6724 Remote Similarity NPD7328 Approved
0.6724 Remote Similarity NPD7327 Approved
0.6723 Remote Similarity NPD8328 Phase 3
0.6667 Remote Similarity NPD7516 Approved
0.6571 Remote Similarity NPD7991 Discontinued
0.6477 Remote Similarity NPD371 Approved
0.6322 Remote Similarity NPD6123 Approved
0.6283 Remote Similarity NPD6412 Phase 2
0.6281 Remote Similarity NPD7503 Approved
0.6271 Remote Similarity NPD6940 Discontinued
0.6228 Remote Similarity NPD8174 Phase 2
0.621 Remote Similarity NPD7507 Approved
0.6124 Remote Similarity NPD8450 Suspended
0.6122 Remote Similarity NPD6115 Approved
0.6122 Remote Similarity NPD6697 Approved
0.6122 Remote Similarity NPD6118 Approved
0.6122 Remote Similarity NPD6114 Approved
0.61 Remote Similarity NPD1780 Approved
0.61 Remote Similarity NPD1779 Approved
0.6087 Remote Similarity NPD6686 Approved
0.6063 Remote Similarity NPD7319 Approved
0.6061 Remote Similarity NPD7645 Phase 2
0.6047 Remote Similarity NPD8449 Approved
0.602 Remote Similarity NPD6116 Phase 1
0.6016 Remote Similarity NPD8517 Approved
0.6016 Remote Similarity NPD8516 Approved
0.6016 Remote Similarity NPD8515 Approved
0.6016 Remote Similarity NPD8513 Phase 3
0.5984 Remote Similarity NPD7736 Approved
0.5948 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5918 Remote Similarity NPD6117 Approved
0.5895 Remote Similarity NPD4787 Phase 1
0.5842 Remote Similarity NPD7525 Registered
0.584 Remote Similarity NPD6370 Approved
0.5833 Remote Similarity NPD8034 Phase 2
0.5833 Remote Similarity NPD8035 Phase 2
0.5816 Remote Similarity NPD3703 Phase 2
0.5814 Remote Similarity NPD7346 Approved
0.5781 Remote Similarity NPD8293 Discontinued
0.5763 Remote Similarity NPD4061 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5698 Remote Similarity NPD887 Approved
0.5698 Remote Similarity NPD888 Phase 3
0.5698 Remote Similarity NPD889 Approved
0.5698 Remote Similarity NPD891 Phase 3
0.5698 Remote Similarity NPD894 Approved
0.5698 Remote Similarity NPD892 Phase 3
0.5698 Remote Similarity NPD895 Approved
0.5698 Remote Similarity NPD893 Approved
0.5698 Remote Similarity NPD890 Clinical (unspecified phase)
0.5682 Remote Similarity NPD2267 Suspended
0.568 Remote Similarity NPD6059 Approved
0.568 Remote Similarity NPD6054 Approved
0.567 Remote Similarity NPD4809 Clinical (unspecified phase)
0.567 Remote Similarity NPD4808 Clinical (unspecified phase)
0.5667 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5625 Remote Similarity NPD3699 Clinical (unspecified phase)
0.5625 Remote Similarity NPD3700 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