Structure

Physi-Chem Properties

Molecular Weight:  870.5
Volume:  850.511
LogP:  3.463
LogD:  3.359
LogS:  -4.176
# Rotatable Bonds:  7
TPSA:  235.68
# H-Bond Aceptor:  16
# H-Bond Donor:  8
# Rings:  9
# Heavy Atoms:  16

MedChem Properties

QED Drug-Likeness Score:  0.169
Synthetic Accessibility Score:  6.662
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:  -5.918
MDCK Permeability:  0.00028604036197066307
Pgp-inhibitor:  0.403
Pgp-substrate:  0.998
Human Intestinal Absorption (HIA):  0.905
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.749

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.007
Plasma Protein Binding (PPB):  58.94622802734375%
Volume Distribution (VD):  0.142
Pgp-substrate:  11.228095054626465%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.792
CYP2C19-inhibitor:  0.004
CYP2C19-substrate:  0.192
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.003
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.054
CYP3A4-inhibitor:  0.027
CYP3A4-substrate:  0.022

ADMET: Excretion

Clearance (CL):  0.977
Half-life (T1/2):  0.691

ADMET: Toxicity

hERG Blockers:  0.991
Human Hepatotoxicity (H-HT):  0.153
Drug-inuced Liver Injury (DILI):  0.365
AMES Toxicity:  0.14
Rat Oral Acute Toxicity:  0.283
Maximum Recommended Daily Dose:  0.033
Skin Sensitization:  0.967
Carcinogencity:  0.299
Eye Corrosion:  0.006
Eye Irritation:  0.01
Respiratory Toxicity:  0.987

Download Data

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

  Natural Product: NPC19400

Natural Product ID:  NPC19400
Common Name*:   KFYOFJUUTSALEH-JLTVVCKYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KFYOFJUUTSALEH-JLTVVCKYSA-N
Standard InCHI:  InChI=1S/C45H74O16/c1-19-9-14-45(54-18-19)20(2)30-28(61-45)16-27-25-8-7-23-15-24(10-12-43(23,5)26(25)11-13-44(27,30)6)57-42-39(60-41-36(52)34(50)32(48)22(4)56-41)37(53)38(29(17-46)58-42)59-40-35(51)33(49)31(47)21(3)55-40/h19-42,46-53H,7-18H2,1-6H3/t19-,20-,21-,22-,23-,24-,25+,26-,27-,28-,29+,30-,31-,32-,33+,34+,35+,36+,37-,38+,39+,40-,41-,42+,43-,44-,45+/m0/s1
SMILES:  OC[C@H]1O[C@@H](O[C@H]2CC[C@]3([C@H](C2)CC[C@@H]2[C@@H]3CC[C@]3([C@H]2C[C@H]2[C@@H]3[C@H](C)[C@]3(O2)CC[C@@H](CO3)C)C)C)[C@@H]([C@H]([C@@H]1O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2036076
PubChem CID:   21607803
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001013] Steroidal glycosides
          • [CHEMONTID:0002364] Steroidal saponins

*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
NPO32523 solanum violaceum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[22413887]
NPO32523 solanum violaceum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[23511021]

☑ 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
NPT65 Cell Line HepG2 Homo sapiens IC50 = 5.33 ug.mL-1 PMID[555504]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 11.57 ug.mL-1 PMID[555504]
NPT81 Cell Line A549 Homo sapiens IC50 = 7.27 ug.mL-1 PMID[555504]
NPT1031 Cell Line Ca9-22 Homo sapiens IC50 = 6.76 ug.mL-1 PMID[555504]
NPT82 Cell Line MDA-MB-231 Homo sapiens IC50 = 8.04 ug.mL-1 PMID[555504]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 3.32 ug.mL-1 PMID[555504]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 2.84 ug.mL-1 PMID[555504]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Inhibition = 38.9 % PMID[555504]

☑ 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 NPC19400 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 NPC473727
1.0 High Similarity NPC6295
1.0 High Similarity NPC206003
1.0 High Similarity NPC473610
1.0 High Similarity NPC107962
1.0 High Similarity NPC107188
1.0 High Similarity NPC475351
1.0 High Similarity NPC211354
0.9888 High Similarity NPC128572
0.9888 High Similarity NPC184617
0.9888 High Similarity NPC132080
0.9888 High Similarity NPC195297
0.9888 High Similarity NPC475643
0.9888 High Similarity NPC84111
0.9888 High Similarity NPC103616
0.9888 High Similarity NPC30856
0.9888 High Similarity NPC232037
0.9888 High Similarity NPC473601
0.9888 High Similarity NPC470866
0.9888 High Similarity NPC475625
0.9888 High Similarity NPC116756
0.9888 High Similarity NPC287483
0.9888 High Similarity NPC470864
0.9888 High Similarity NPC97700
0.9888 High Similarity NPC160426
0.9888 High Similarity NPC284104
0.9888 High Similarity NPC98018
0.9888 High Similarity NPC470865
0.9888 High Similarity NPC470863
0.9886 High Similarity NPC291203
0.9886 High Similarity NPC471464
0.9886 High Similarity NPC264101
0.9886 High Similarity NPC217205
0.9778 High Similarity NPC476112
0.9778 High Similarity NPC307534
0.9778 High Similarity NPC470861
0.9778 High Similarity NPC274200
0.9778 High Similarity NPC232611
0.9778 High Similarity NPC115165
0.9778 High Similarity NPC303069
0.9778 High Similarity NPC83137
0.9778 High Similarity NPC470862
0.9778 High Similarity NPC51520
0.9773 High Similarity NPC477451
0.9773 High Similarity NPC325828
0.9773 High Similarity NPC177834
0.9773 High Similarity NPC477547
0.9773 High Similarity NPC141769
0.9773 High Similarity NPC250393
0.9773 High Similarity NPC249204
0.9773 High Similarity NPC234352
0.9773 High Similarity NPC48339
0.9773 High Similarity NPC297348
0.967 High Similarity NPC473518
0.967 High Similarity NPC291548
0.9667 High Similarity NPC139271
0.9667 High Similarity NPC304011
0.9667 High Similarity NPC121453
0.9663 High Similarity NPC131693
0.9663 High Similarity NPC294686
0.9663 High Similarity NPC222731
0.9663 High Similarity NPC473851
0.9663 High Similarity NPC174024
0.9663 High Similarity NPC291547
0.9663 High Similarity NPC312678
0.9663 High Similarity NPC253268
0.9663 High Similarity NPC179859
0.9663 High Similarity NPC475436
0.9556 High Similarity NPC474399
0.9551 High Similarity NPC137004
0.9551 High Similarity NPC88962
0.9551 High Similarity NPC144790
0.9551 High Similarity NPC149400
0.9551 High Similarity NPC172838
0.9444 High Similarity NPC473774
0.9444 High Similarity NPC252253
0.9444 High Similarity NPC45959
0.9444 High Similarity NPC305418
0.9444 High Similarity NPC24960
0.9348 High Similarity NPC477223
0.9348 High Similarity NPC477222
0.9326 High Similarity NPC473542
0.9326 High Similarity NPC65550
0.9239 High Similarity NPC476510
0.9239 High Similarity NPC142264
0.9222 High Similarity NPC5632
0.9222 High Similarity NPC204881
0.9222 High Similarity NPC473830
0.9222 High Similarity NPC210759
0.9222 High Similarity NPC307167
0.9222 High Similarity NPC149966
0.9222 High Similarity NPC229801
0.914 High Similarity NPC475207
0.914 High Similarity NPC233649
0.914 High Similarity NPC470028
0.914 High Similarity NPC470591
0.914 High Similarity NPC210157
0.9121 High Similarity NPC473726
0.9121 High Similarity NPC167644
0.9121 High Similarity NPC311246
0.9101 High Similarity NPC281004
0.9053 High Similarity NPC475574
0.9043 High Similarity NPC473616
0.9022 High Similarity NPC3538
0.9022 High Similarity NPC309866
0.9022 High Similarity NPC175
0.9022 High Similarity NPC477224
0.9022 High Similarity NPC113500
0.9 High Similarity NPC20822
0.9 High Similarity NPC82955
0.9 High Similarity NPC102725
0.9 High Similarity NPC131466
0.9 High Similarity NPC473472
0.8925 High Similarity NPC92196
0.8925 High Similarity NPC473064
0.8925 High Similarity NPC477494
0.8925 High Similarity NPC473065
0.8925 High Similarity NPC473067
0.8901 High Similarity NPC279329
0.8901 High Similarity NPC223143
0.8889 High Similarity NPC92890
0.8889 High Similarity NPC202898
0.8889 High Similarity NPC475319
0.8889 High Similarity NPC49032
0.8889 High Similarity NPC125324
0.8889 High Similarity NPC51172
0.8854 High Similarity NPC476512
0.8854 High Similarity NPC472081
0.8854 High Similarity NPC108227
0.8842 High Similarity NPC473638
0.883 High Similarity NPC237071
0.883 High Similarity NPC203434
0.883 High Similarity NPC238796
0.883 High Similarity NPC296936
0.8817 High Similarity NPC77717
0.8817 High Similarity NPC471373
0.8817 High Similarity NPC253611
0.8817 High Similarity NPC267238
0.8817 High Similarity NPC148593
0.8804 High Similarity NPC293609
0.8804 High Similarity NPC36372
0.8804 High Similarity NPC473637
0.8804 High Similarity NPC476668
0.88 High Similarity NPC220836
0.88 High Similarity NPC151134
0.88 High Similarity NPC233433
0.88 High Similarity NPC473817
0.88 High Similarity NPC94086
0.88 High Similarity NPC92297
0.88 High Similarity NPC273002
0.8778 High Similarity NPC43912
0.8778 High Similarity NPC140446
0.8763 High Similarity NPC470029
0.8763 High Similarity NPC310138
0.8763 High Similarity NPC80191
0.8763 High Similarity NPC114700
0.8763 High Similarity NPC134967
0.8763 High Similarity NPC310031
0.8723 High Similarity NPC471425
0.8723 High Similarity NPC189575
0.8723 High Similarity NPC471429
0.8723 High Similarity NPC205129
0.8723 High Similarity NPC471424
0.8723 High Similarity NPC106701
0.8713 High Similarity NPC470867
0.871 High Similarity NPC18724
0.871 High Similarity NPC470623
0.871 High Similarity NPC323231
0.871 High Similarity NPC476669
0.871 High Similarity NPC277774
0.871 High Similarity NPC224003
0.871 High Similarity NPC171741
0.8687 High Similarity NPC215408
0.8673 High Similarity NPC476837
0.8673 High Similarity NPC97260
0.8673 High Similarity NPC139181
0.866 High Similarity NPC476839
0.866 High Similarity NPC476838
0.866 High Similarity NPC477225
0.8652 High Similarity NPC227260
0.8617 High Similarity NPC475325
0.8617 High Similarity NPC30687
0.8617 High Similarity NPC473503
0.8602 High Similarity NPC59006
0.86 High Similarity NPC54619
0.8557 High Similarity NPC20028
0.8556 High Similarity NPC290612
0.8556 High Similarity NPC232044
0.8556 High Similarity NPC273290
0.8526 High Similarity NPC57964
0.8526 High Similarity NPC94582
0.8526 High Similarity NPC469710
0.8515 High Similarity NPC128123
0.8454 Intermediate Similarity NPC209798
0.8454 Intermediate Similarity NPC471375
0.8454 Intermediate Similarity NPC471374
0.8447 Intermediate Similarity NPC92710
0.8447 Intermediate Similarity NPC476547
0.8438 Intermediate Similarity NPC473287
0.8431 Intermediate Similarity NPC300557

  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 NPC19400 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
0.9773 High Similarity NPD8171 Discontinued
0.8776 High Similarity NPD8170 Clinical (unspecified phase)
0.8409 Intermediate Similarity NPD6928 Phase 2
0.7615 Intermediate Similarity NPD8133 Approved
0.7522 Intermediate Similarity NPD8377 Approved
0.7522 Intermediate Similarity NPD8294 Approved
0.7456 Intermediate Similarity NPD8378 Approved
0.7456 Intermediate Similarity NPD8296 Approved
0.7456 Intermediate Similarity NPD8380 Approved
0.7456 Intermediate Similarity NPD8335 Approved
0.7456 Intermediate Similarity NPD8379 Approved
0.7426 Intermediate Similarity NPD7991 Discontinued
0.7304 Intermediate Similarity NPD8033 Approved
0.7043 Intermediate Similarity NPD7328 Approved
0.7043 Intermediate Similarity NPD7327 Approved
0.6983 Remote Similarity NPD7516 Approved
0.6935 Remote Similarity NPD8450 Suspended
0.6889 Remote Similarity NPD4267 Clinical (unspecified phase)
0.6855 Remote Similarity NPD8449 Approved
0.6774 Remote Similarity NPD1810 Approved
0.6774 Remote Similarity NPD1811 Approved
0.6757 Remote Similarity NPD6412 Phase 2
0.6639 Remote Similarity NPD7507 Approved
0.6637 Remote Similarity NPD8132 Clinical (unspecified phase)
0.6583 Remote Similarity NPD7503 Approved
0.6581 Remote Similarity NPD6940 Discontinued
0.6549 Remote Similarity NPD8174 Phase 2
0.6525 Remote Similarity NPD8295 Clinical (unspecified phase)
0.648 Remote Similarity NPD7319 Approved
0.6452 Remote Similarity NPD4787 Phase 1
0.6452 Remote Similarity NPD2687 Approved
0.6452 Remote Similarity NPD2254 Approved
0.6452 Remote Similarity NPD2686 Approved
0.64 Remote Similarity NPD7736 Approved
0.6364 Remote Similarity NPD6123 Approved
0.6341 Remote Similarity NPD8328 Phase 3
0.6337 Remote Similarity NPD3669 Approved
0.6337 Remote Similarity NPD3670 Clinical (unspecified phase)
0.6327 Remote Similarity NPD6697 Approved
0.6327 Remote Similarity NPD6118 Approved
0.6327 Remote Similarity NPD6115 Approved
0.6327 Remote Similarity NPD6114 Approved
0.6277 Remote Similarity NPD7532 Clinical (unspecified phase)
0.626 Remote Similarity NPD6370 Approved
0.6224 Remote Similarity NPD6116 Phase 1
0.619 Remote Similarity NPD8293 Discontinued
0.6122 Remote Similarity NPD6117 Approved
0.6098 Remote Similarity NPD6054 Approved
0.6098 Remote Similarity NPD6059 Approved
0.6082 Remote Similarity NPD6113 Clinical (unspecified phase)
0.6042 Remote Similarity NPD4809 Clinical (unspecified phase)
0.6042 Remote Similarity NPD4808 Clinical (unspecified phase)
0.5983 Remote Similarity NPD6686 Approved
0.5978 Remote Similarity NPD371 Approved
0.5952 Remote Similarity NPD6067 Discontinued
0.5938 Remote Similarity NPD4244 Approved
0.5938 Remote Similarity NPD4245 Approved
0.592 Remote Similarity NPD6016 Approved
0.592 Remote Similarity NPD6015 Approved
0.5906 Remote Similarity NPD7492 Approved
0.5882 Remote Similarity NPD7525 Registered
0.5873 Remote Similarity NPD5988 Approved
0.5872 Remote Similarity NPD8034 Phase 2
0.5872 Remote Similarity NPD8035 Phase 2
0.5862 Remote Similarity NPD4057 Clinical (unspecified phase)
0.5862 Remote Similarity NPD4056 Clinical (unspecified phase)
0.5859 Remote Similarity NPD3702 Approved
0.5859 Remote Similarity NPD6616 Approved
0.5859 Remote Similarity NPD3703 Phase 2
0.5857 Remote Similarity NPD7625 Phase 1
0.5833 Remote Similarity NPD3698 Phase 2
0.5833 Remote Similarity NPD3700 Clinical (unspecified phase)
0.5833 Remote Similarity NPD3699 Clinical (unspecified phase)
0.5814 Remote Similarity NPD7078 Approved
0.5794 Remote Similarity NPD8516 Approved
0.5794 Remote Similarity NPD8517 Approved
0.5794 Remote Similarity NPD8515 Approved
0.5739 Remote Similarity NPD1700 Approved
0.573 Remote Similarity NPD2267 Suspended
0.5714 Remote Similarity NPD5777 Approved
0.5702 Remote Similarity NPD7638 Approved
0.5682 Remote Similarity NPD7346 Approved
0.5673 Remote Similarity NPD1779 Approved
0.5673 Remote Similarity NPD1780 Approved
0.5669 Remote Similarity NPD8513 Phase 3
0.5656 Remote Similarity NPD6882 Approved
0.5656 Remote Similarity NPD8297 Approved
0.5652 Remote Similarity NPD7640 Approved
0.5652 Remote Similarity NPD7639 Approved
0.5649 Remote Similarity NPD6033 Approved
0.5648 Remote Similarity NPD7524 Approved
0.5631 Remote Similarity NPD7645 Phase 2
0.563 Remote Similarity NPD7646 Clinical (unspecified phase)
0.5612 Remote Similarity NPD4789 Approved
0.5607 Remote Similarity NPD7520 Clinical (unspecified phase)
0.56 Remote Similarity NPD6009 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