Structure

Physi-Chem Properties

Molecular Weight:  326.2
Volume:  340.722
LogP:  3.131
LogD:  2.959
LogS:  -2.905
# Rotatable Bonds:  1
TPSA:  48.49
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  5
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.847
Synthetic Accessibility Score:  5.046
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.368
MDCK Permeability:  7.063927569106454e-06
Pgp-inhibitor:  0.981
Pgp-substrate:  0.98
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.026
30% Bioavailability (F30%):  0.006

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.385
Plasma Protein Binding (PPB):  59.32638931274414%
Volume Distribution (VD):  4.194
Pgp-substrate:  30.61811065673828%

ADMET: Metabolism

CYP1A2-inhibitor:  0.208
CYP1A2-substrate:  0.69
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.825
CYP2C9-inhibitor:  0.022
CYP2C9-substrate:  0.139
CYP2D6-inhibitor:  0.629
CYP2D6-substrate:  0.896
CYP3A4-inhibitor:  0.123
CYP3A4-substrate:  0.83

ADMET: Excretion

Clearance (CL):  9.307
Half-life (T1/2):  0.496

ADMET: Toxicity

hERG Blockers:  0.12
Human Hepatotoxicity (H-HT):  0.353
Drug-inuced Liver Injury (DILI):  0.931
AMES Toxicity:  0.054
Rat Oral Acute Toxicity:  0.907
Maximum Recommended Daily Dose:  0.977
Skin Sensitization:  0.24
Carcinogencity:  0.635
Eye Corrosion:  0.111
Eye Irritation:  0.174
Respiratory Toxicity:  0.984

Download Data

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

  Natural Product: NPC139271

Natural Product ID:  NPC139271
Common Name*:   Operculinoside D
IUPAC Name:   (2S,3R,4S,5S,6R)-2-[(2R,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-[[(3S,5R,8R,9R,10R,13R,14R,16R,17R)-16-hydroxy-4,4,8,10,14-pentamethyl-17-[(2S,5S)-2-methyl-5-[2-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxypropan-2-yl]oxolan-2-yl]-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-yl]oxy]oxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms:   Operculinoside D
Standard InCHIKey:  OHBOIROQVADHLU-COBIJELOSA-N
Standard InCHI:  InChI=1S/C48H82O19/c1-43(2)26-11-15-46(6)27(45(26,5)14-12-28(43)64-42-39(36(58)33(55)25(20-51)63-42)65-40-37(59)34(56)31(53)23(18-49)61-40)10-9-21-30(22(52)17-47(21,46)7)48(8)16-13-29(66-48)44(3,4)67-41-38(60)35(57)32(54)24(19-50)62-41/h21-42,49-60H,9-20H2,1-8H3/t21-,22-,23-,24-,25-,26+,27-,28+,29+,30-,31-,32-,33-,34+,35+,36+,37-,38-,39-,40+,41+,42+,45+,46-,47-,48+/m1/s1
SMILES:  CC1(C)[C@@H]2CC[C@]3(C)[C@H](CC[C@@H]4[C@H]([C@@H](C[C@@]34C)O)[C@]3(C)CC[C@@H](C(C)(C)O[C@H]4[C@@H]([C@H]([C@@H]([C@@H](CO)O4)O)O)O)O3)[C@@]2(C)CC[C@@H]1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1910829
PubChem CID:   54671550
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001580] Triterpene glycosides
            • [CHEMONTID:0002358] Triterpene 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
NPO10224 Operculina turpethum Species Convolvulaceae Eukaryota n.a. aerial part n.a. PMID[21866900]
NPO10224 Operculina turpethum Species Convolvulaceae 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Inhibition = 22.2 % PMID[513993]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Inhibition = 6.3 % PMID[513993]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Inhibition = 5.5 % PMID[513993]
NPT27 Others Unspecified MTD = 100.0 ug ml-1 PMID[513993]

☑ 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 NPC139271 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 NPC304011
0.9778 High Similarity NPC121453
0.9775 High Similarity NPC305418
0.9775 High Similarity NPC291547
0.9775 High Similarity NPC174024
0.9775 High Similarity NPC253268
0.9775 High Similarity NPC217205
0.9775 High Similarity NPC45959
0.9775 High Similarity NPC252253
0.9775 High Similarity NPC179859
0.9775 High Similarity NPC291203
0.9775 High Similarity NPC475436
0.9775 High Similarity NPC131693
0.9775 High Similarity NPC473851
0.9775 High Similarity NPC312678
0.967 High Similarity NPC477223
0.967 High Similarity NPC274200
0.967 High Similarity NPC307534
0.967 High Similarity NPC477222
0.967 High Similarity NPC476112
0.9667 High Similarity NPC19400
0.9667 High Similarity NPC474399
0.9667 High Similarity NPC206003
0.9667 High Similarity NPC473727
0.9667 High Similarity NPC107188
0.9667 High Similarity NPC211354
0.9667 High Similarity NPC473610
0.9667 High Similarity NPC475351
0.9667 High Similarity NPC6295
0.9667 High Similarity NPC107962
0.9663 High Similarity NPC144790
0.9663 High Similarity NPC297348
0.9663 High Similarity NPC149400
0.9663 High Similarity NPC249204
0.9663 High Similarity NPC88962
0.9663 High Similarity NPC172838
0.9663 High Similarity NPC234352
0.9663 High Similarity NPC177834
0.9663 High Similarity NPC477547
0.9663 High Similarity NPC141769
0.9663 High Similarity NPC477451
0.9663 High Similarity NPC325828
0.9663 High Similarity NPC250393
0.9663 High Similarity NPC48339
0.9663 High Similarity NPC137004
0.9565 High Similarity NPC473518
0.956 High Similarity NPC128572
0.956 High Similarity NPC142264
0.956 High Similarity NPC98018
0.956 High Similarity NPC470864
0.956 High Similarity NPC30856
0.956 High Similarity NPC116756
0.956 High Similarity NPC97700
0.956 High Similarity NPC103616
0.956 High Similarity NPC184617
0.956 High Similarity NPC132080
0.956 High Similarity NPC287483
0.956 High Similarity NPC470863
0.956 High Similarity NPC195297
0.956 High Similarity NPC475643
0.956 High Similarity NPC476510
0.956 High Similarity NPC84111
0.956 High Similarity NPC232037
0.956 High Similarity NPC473601
0.956 High Similarity NPC475625
0.956 High Similarity NPC470865
0.956 High Similarity NPC284104
0.956 High Similarity NPC470866
0.956 High Similarity NPC160426
0.9556 High Similarity NPC471464
0.9556 High Similarity NPC222731
0.9556 High Similarity NPC473774
0.9556 High Similarity NPC294686
0.9556 High Similarity NPC264101
0.9556 High Similarity NPC24960
0.9551 High Similarity NPC229801
0.9551 High Similarity NPC307167
0.9551 High Similarity NPC210759
0.9457 High Similarity NPC232611
0.9457 High Similarity NPC83137
0.9457 High Similarity NPC115165
0.9457 High Similarity NPC470862
0.9457 High Similarity NPC470028
0.9457 High Similarity NPC303069
0.9457 High Similarity NPC233649
0.9457 High Similarity NPC470861
0.9457 High Similarity NPC51520
0.9444 High Similarity NPC167644
0.9444 High Similarity NPC311246
0.9438 High Similarity NPC473542
0.9438 High Similarity NPC65550
0.9362 High Similarity NPC475574
0.9355 High Similarity NPC291548
0.9341 High Similarity NPC477224
0.9341 High Similarity NPC175
0.9341 High Similarity NPC113500
0.9341 High Similarity NPC3538
0.9341 High Similarity NPC309866
0.9333 High Similarity NPC473830
0.9333 High Similarity NPC204881
0.9333 High Similarity NPC5632
0.9333 High Similarity NPC149966
0.9326 High Similarity NPC82955
0.9326 High Similarity NPC131466
0.9247 High Similarity NPC475207
0.9247 High Similarity NPC470591
0.9239 High Similarity NPC473064
0.9239 High Similarity NPC473067
0.9239 High Similarity NPC92196
0.9239 High Similarity NPC473065
0.9231 High Similarity NPC473726
0.9222 High Similarity NPC279329
0.9213 High Similarity NPC281004
0.9158 High Similarity NPC476512
0.9158 High Similarity NPC472081
0.9158 High Similarity NPC108227
0.9149 High Similarity NPC473616
0.9149 High Similarity NPC473638
0.914 High Similarity NPC237071
0.914 High Similarity NPC238796
0.914 High Similarity NPC203434
0.9121 High Similarity NPC36372
0.9121 High Similarity NPC293609
0.9111 High Similarity NPC473472
0.9111 High Similarity NPC20822
0.9111 High Similarity NPC102725
0.9101 High Similarity NPC140446
0.9101 High Similarity NPC43912
0.9062 High Similarity NPC114700
0.9062 High Similarity NPC310138
0.9062 High Similarity NPC470029
0.9062 High Similarity NPC134967
0.9043 High Similarity NPC210157
0.9032 High Similarity NPC477494
0.9022 High Similarity NPC224003
0.9022 High Similarity NPC277774
0.9022 High Similarity NPC171741
0.9022 High Similarity NPC323231
0.9022 High Similarity NPC470623
0.9022 High Similarity NPC18724
0.9011 High Similarity NPC223143
0.8969 High Similarity NPC97260
0.8969 High Similarity NPC476837
0.8969 High Similarity NPC139181
0.8958 High Similarity NPC476839
0.8958 High Similarity NPC476838
0.8958 High Similarity NPC477225
0.8936 High Similarity NPC296936
0.8925 High Similarity NPC77717
0.8925 High Similarity NPC30687
0.8925 High Similarity NPC473503
0.8925 High Similarity NPC267238
0.8925 High Similarity NPC253611
0.8925 High Similarity NPC471373
0.8925 High Similarity NPC148593
0.8913 High Similarity NPC59006
0.8913 High Similarity NPC473637
0.8913 High Similarity NPC476668
0.8876 High Similarity NPC290612
0.883 High Similarity NPC471424
0.883 High Similarity NPC471429
0.883 High Similarity NPC106701
0.883 High Similarity NPC189575
0.883 High Similarity NPC469710
0.883 High Similarity NPC471425
0.883 High Similarity NPC94582
0.883 High Similarity NPC57964
0.883 High Similarity NPC205129
0.8817 High Similarity NPC476669
0.8737 High Similarity NPC473287
0.8723 High Similarity NPC475325
0.8696 High Similarity NPC228059
0.8681 High Similarity NPC210658
0.8681 High Similarity NPC161928
0.8681 High Similarity NPC472396
0.8673 High Similarity NPC310031
0.8673 High Similarity NPC80191
0.8667 High Similarity NPC232044
0.8667 High Similarity NPC273290
0.866 High Similarity NPC470030
0.8614 High Similarity NPC49032
0.8614 High Similarity NPC202898
0.8614 High Similarity NPC475319
0.8614 High Similarity NPC51172
0.8614 High Similarity NPC125324
0.8614 High Similarity NPC92890
0.8614 High Similarity NPC220427
0.86 High Similarity NPC215408
0.8587 High Similarity NPC128475
0.8571 High Similarity NPC477172
0.8558 High Similarity NPC476693
0.8557 High Similarity NPC209798
0.8557 High Similarity NPC471375
0.8557 High Similarity NPC471374
0.8556 High Similarity NPC227260
0.8542 High Similarity NPC156377
0.8539 High Similarity NPC296734
0.8539 High Similarity NPC470611
0.8529 High Similarity NPC151134
0.8529 High Similarity NPC473817

  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 NPC139271 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
0.9663 High Similarity NPD8171 Discontinued
0.8687 High Similarity NPD8170 Clinical (unspecified phase)
0.8315 Intermediate Similarity NPD6928 Phase 2
0.7768 Intermediate Similarity NPD8294 Approved
0.7768 Intermediate Similarity NPD8377 Approved
0.7706 Intermediate Similarity NPD8133 Approved
0.7699 Intermediate Similarity NPD8378 Approved
0.7699 Intermediate Similarity NPD8296 Approved
0.7699 Intermediate Similarity NPD8335 Approved
0.7699 Intermediate Similarity NPD8380 Approved
0.7699 Intermediate Similarity NPD8379 Approved
0.7544 Intermediate Similarity NPD8033 Approved
0.7353 Intermediate Similarity NPD7991 Discontinued
0.7281 Intermediate Similarity NPD7328 Approved
0.7281 Intermediate Similarity NPD7327 Approved
0.7217 Intermediate Similarity NPD7516 Approved
0.7191 Intermediate Similarity NPD4267 Clinical (unspecified phase)
0.7065 Intermediate Similarity NPD1810 Approved
0.7065 Intermediate Similarity NPD1811 Approved
0.686 Remote Similarity NPD7507 Approved
0.6807 Remote Similarity NPD7503 Approved
0.6746 Remote Similarity NPD8450 Suspended
0.6739 Remote Similarity NPD2687 Approved
0.6739 Remote Similarity NPD2254 Approved
0.6739 Remote Similarity NPD2686 Approved
0.6726 Remote Similarity NPD8132 Clinical (unspecified phase)
0.6696 Remote Similarity NPD6412 Phase 2
0.6694 Remote Similarity NPD7319 Approved
0.6667 Remote Similarity NPD8449 Approved
0.6613 Remote Similarity NPD7736 Approved
0.661 Remote Similarity NPD8295 Clinical (unspecified phase)
0.66 Remote Similarity NPD3670 Clinical (unspecified phase)
0.66 Remote Similarity NPD3669 Approved
0.6559 Remote Similarity NPD4787 Phase 1
0.6525 Remote Similarity NPD6940 Discontinued
0.6491 Remote Similarity NPD8174 Phase 2
0.6475 Remote Similarity NPD6370 Approved
0.6429 Remote Similarity NPD6115 Approved
0.6429 Remote Similarity NPD6697 Approved
0.6429 Remote Similarity NPD6114 Approved
0.6429 Remote Similarity NPD6118 Approved
0.6423 Remote Similarity NPD8328 Phase 3
0.64 Remote Similarity NPD8293 Discontinued
0.6383 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6327 Remote Similarity NPD6116 Phase 1
0.6311 Remote Similarity NPD6054 Approved
0.6311 Remote Similarity NPD6059 Approved
0.6264 Remote Similarity NPD371 Approved
0.6224 Remote Similarity NPD6117 Approved
0.6139 Remote Similarity NPD7525 Registered
0.6129 Remote Similarity NPD6015 Approved
0.6129 Remote Similarity NPD6016 Approved
0.6111 Remote Similarity NPD7492 Approved
0.6111 Remote Similarity NPD6123 Approved
0.608 Remote Similarity NPD5988 Approved
0.6063 Remote Similarity NPD6616 Approved
0.6043 Remote Similarity NPD7625 Phase 1
0.6032 Remote Similarity NPD6067 Discontinued
0.602 Remote Similarity NPD6113 Clinical (unspecified phase)
0.6016 Remote Similarity NPD7078 Approved
0.5979 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5979 Remote Similarity NPD4808 Clinical (unspecified phase)
0.5965 Remote Similarity NPD1700 Approved
0.5963 Remote Similarity NPD8034 Phase 2
0.5963 Remote Similarity NPD8035 Phase 2
0.596 Remote Similarity NPD3703 Phase 2
0.596 Remote Similarity NPD3702 Approved
0.5948 Remote Similarity NPD4057 Clinical (unspecified phase)
0.5948 Remote Similarity NPD4056 Clinical (unspecified phase)
0.5932 Remote Similarity NPD6686 Approved
0.5922 Remote Similarity NPD1780 Approved
0.5922 Remote Similarity NPD1779 Approved
0.5876 Remote Similarity NPD4245 Approved
0.5876 Remote Similarity NPD4244 Approved
0.5873 Remote Similarity NPD8517 Approved
0.5873 Remote Similarity NPD8513 Phase 3
0.5873 Remote Similarity NPD8516 Approved
0.5873 Remote Similarity NPD8515 Approved
0.5868 Remote Similarity NPD8297 Approved
0.5868 Remote Similarity NPD6882 Approved
0.5846 Remote Similarity NPD6033 Approved
0.5806 Remote Similarity NPD6009 Approved
0.5794 Remote Similarity NPD6319 Approved
0.5789 Remote Similarity NPD7638 Approved
0.5773 Remote Similarity NPD3700 Clinical (unspecified phase)
0.5773 Remote Similarity NPD3698 Phase 2
0.5773 Remote Similarity NPD3699 Clinical (unspecified phase)
0.5741 Remote Similarity NPD7524 Approved
0.5739 Remote Similarity NPD7639 Approved
0.5739 Remote Similarity NPD7640 Approved
0.5728 Remote Similarity NPD7645 Phase 2
0.5701 Remote Similarity NPD7520 Clinical (unspecified phase)
0.5691 Remote Similarity NPD4632 Approved
0.567 Remote Similarity NPD5360 Phase 3
0.567 Remote Similarity NPD5361 Clinical (unspecified phase)
0.5667 Remote Similarity NPD2267 Suspended
0.5667 Remote Similarity NPD7320 Approved
0.5667 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5657 Remote Similarity NPD5777 Approved
0.5648 Remote Similarity NPD8308 Discontinued
0.5641 Remote Similarity NPD7632 Discontinued
0.563 Remote Similarity NPD7128 Approved
0.563 Remote Similarity NPD6402 Approved
0.563 Remote Similarity NPD5739 Approved
0.563 Remote Similarity NPD6675 Approved
0.562 Remote Similarity NPD6372 Approved
0.562 Remote Similarity NPD6373 Approved
0.5618 Remote Similarity NPD7346 Approved
0.5607 Remote Similarity NPD7338 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