Structure

Physi-Chem Properties

Molecular Weight:  877.7
Volume:  976.318
LogP:  9.278
LogD:  5.276
LogS:  -1.887
# Rotatable Bonds:  42
TPSA:  168.94
# H-Bond Aceptor:  10
# H-Bond Donor:  7
# Rings:  1
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.014
Synthetic Accessibility Score:  5.305
Fsp3:  0.827
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:  -5.554
MDCK Permeability:  9.67314190347679e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.018
Human Intestinal Absorption (HIA):  0.916
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  104.3265151977539%
Volume Distribution (VD):  0.765
Pgp-substrate:  0.9734548330307007%

ADMET: Metabolism

CYP1A2-inhibitor:  0.015
CYP1A2-substrate:  0.139
CYP2C19-inhibitor:  0.084
CYP2C19-substrate:  0.03
CYP2C9-inhibitor:  0.044
CYP2C9-substrate:  0.998
CYP2D6-inhibitor:  0.759
CYP2D6-substrate:  0.684
CYP3A4-inhibitor:  0.253
CYP3A4-substrate:  0.007

ADMET: Excretion

Clearance (CL):  2.163
Half-life (T1/2):  0.606

ADMET: Toxicity

hERG Blockers:  0.927
Human Hepatotoxicity (H-HT):  0.125
Drug-inuced Liver Injury (DILI):  0.005
AMES Toxicity:  0.065
Rat Oral Acute Toxicity:  0.016
Maximum Recommended Daily Dose:  0.897
Skin Sensitization:  0.977
Carcinogencity:  0.008
Eye Corrosion:  0.003
Eye Irritation:  0.008
Respiratory Toxicity:  0.6

Download Data

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

  Natural Product: NPC8098

Natural Product ID:  NPC8098
Common Name*:   Renieroside B3
IUPAC Name:   (Z,2R)-2-hydroxy-N-[(2S,3R,4E,8E,10E)-3-hydroxy-9-methyl-1-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoctadeca-4,8,10-trien-2-yl]heptacos-20-enamide
Synonyms:   renieroside B3
Standard InCHIKey:  XBGQJELPFUYHAI-IVFQGWKFSA-N
Standard InCHI:  InChI=1S/C52H95NO9/c1-4-6-8-10-12-13-14-15-16-17-18-19-20-21-22-23-24-25-26-27-29-31-35-40-46(56)51(60)53-44(42-61-52-50(59)49(58)48(57)47(41-54)62-52)45(55)39-36-32-34-38-43(3)37-33-30-28-11-9-7-5-2/h13-14,33,36-39,44-50,52,54-59H,4-12,15-32,34-35,40-42H2,1-3H3,(H,53,60)/b14-13-,37-33+,39-36+,43-38+/t44-,45+,46+,47+,48+,49-,50+,52+/m0/s1
SMILES:  CCCCCC/C=CCCCCCCCCCCCCCCCCC[C@H](C(=N[C@@H](CO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)[C@@H](/C=C/CC/C=C(C)/C=C/CCCCCCC)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL249051
PubChem CID:   23643542
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000257] Sphingolipids
        • [CHEMONTID:0003258] Glycosphingolipids
          • [CHEMONTID:0001419] Neutral glycosphingolipids
            • [CHEMONTID:0001428] Simple glycosylceramides
              • [CHEMONTID:0004305] Glycosyl-N-acylsphingosines

*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
NPO33502 Haliclona sp. Species Chalinidae Eukaryota n.a. n.a. n.a. PMID[11575970]
NPO33502 Haliclona sp. Species Chalinidae Eukaryota n.a. n.a. n.a. PMID[17848089]
NPO33502 Haliclona sp. Species Chalinidae Eukaryota n.a. Pacific n.a. PMID[19133758]
NPO33502 Haliclona sp. Species Chalinidae Eukaryota n.a. Culasian Point, Leyte, Philippines (S 1119.00', E 12435.60') 1991-MAR PMID[22873824]
NPO33502 Haliclona sp. Species Chalinidae Eukaryota n.a. New Zealand n.a. PMID[24128145]

☑ 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
NPT81 Cell Line A549 Homo sapiens ED50 > 10.0 ug ml-1 PMID[544337]
NPT146 Cell Line SK-OV-3 Homo sapiens ED50 > 10.0 ug ml-1 PMID[544337]
NPT147 Cell Line SK-MEL-2 Homo sapiens ED50 > 10.0 ug ml-1 PMID[544337]
NPT574 Cell Line XF498 Homo sapiens ED50 > 10.0 ug ml-1 PMID[544337]
NPT148 Cell Line HCT-15 Homo sapiens ED50 > 10.0 ug ml-1 PMID[544337]

☑ 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 NPC8098 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 NPC183449
1.0 High Similarity NPC197294
0.9778 High Similarity NPC45313
0.9775 High Similarity NPC156782
0.9775 High Similarity NPC256570
0.9775 High Similarity NPC157353
0.9775 High Similarity NPC192066
0.9775 High Similarity NPC54961
0.9775 High Similarity NPC158445
0.9775 High Similarity NPC282088
0.9775 High Similarity NPC3568
0.9775 High Similarity NPC17290
0.9556 High Similarity NPC262312
0.9556 High Similarity NPC23454
0.9556 High Similarity NPC35269
0.9556 High Similarity NPC70323
0.9551 High Similarity NPC473581
0.9551 High Similarity NPC15851
0.9551 High Similarity NPC473950
0.9551 High Similarity NPC309898
0.9551 High Similarity NPC111567
0.9551 High Similarity NPC186840
0.9551 High Similarity NPC473604
0.9551 High Similarity NPC475125
0.9551 High Similarity NPC263545
0.9438 High Similarity NPC242503
0.9438 High Similarity NPC74672
0.9438 High Similarity NPC209047
0.9438 High Similarity NPC139782
0.9438 High Similarity NPC43074
0.9333 High Similarity NPC282705
0.9333 High Similarity NPC182632
0.8913 High Similarity NPC475603
0.8913 High Similarity NPC61894
0.86 High Similarity NPC201128
0.83 Intermediate Similarity NPC477198
0.7714 Intermediate Similarity NPC475918
0.764 Intermediate Similarity NPC288086
0.7624 Intermediate Similarity NPC475503
0.7549 Intermediate Similarity NPC475646
0.7523 Intermediate Similarity NPC29501
0.7396 Intermediate Similarity NPC476523
0.7358 Intermediate Similarity NPC55336
0.729 Intermediate Similarity NPC74035
0.7191 Intermediate Similarity NPC291196
0.7191 Intermediate Similarity NPC103712
0.7174 Intermediate Similarity NPC264417
0.7174 Intermediate Similarity NPC217095
0.7156 Intermediate Similarity NPC315426
0.7143 Intermediate Similarity NPC55652
0.7143 Intermediate Similarity NPC314678
0.7129 Intermediate Similarity NPC477866
0.7129 Intermediate Similarity NPC477865
0.7115 Intermediate Similarity NPC189629
0.7113 Intermediate Similarity NPC228638
0.7075 Intermediate Similarity NPC271207
0.7075 Intermediate Similarity NPC255175
0.7075 Intermediate Similarity NPC206711
0.7075 Intermediate Similarity NPC225978
0.7071 Intermediate Similarity NPC208473
0.7034 Intermediate Similarity NPC469943
0.703 Intermediate Similarity NPC39290
0.703 Intermediate Similarity NPC159369
0.6952 Remote Similarity NPC175614
0.6915 Remote Similarity NPC229655
0.6882 Remote Similarity NPC472173
0.6869 Remote Similarity NPC473308
0.6842 Remote Similarity NPC314306
0.6832 Remote Similarity NPC475186
0.6832 Remote Similarity NPC118077
0.6804 Remote Similarity NPC127295
0.6804 Remote Similarity NPC163362
0.68 Remote Similarity NPC73166
0.6786 Remote Similarity NPC475150
0.6777 Remote Similarity NPC313333
0.6777 Remote Similarity NPC314512
0.6777 Remote Similarity NPC314451
0.6777 Remote Similarity NPC313342
0.6771 Remote Similarity NPC474833
0.6768 Remote Similarity NPC473315
0.6768 Remote Similarity NPC142111
0.6765 Remote Similarity NPC470284
0.6748 Remote Similarity NPC329919
0.6748 Remote Similarity NPC477793
0.6735 Remote Similarity NPC236649
0.6735 Remote Similarity NPC21693
0.6735 Remote Similarity NPC469469
0.6731 Remote Similarity NPC472199
0.6731 Remote Similarity NPC472197
0.6702 Remote Similarity NPC472174
0.67 Remote Similarity NPC477199
0.6696 Remote Similarity NPC469865
0.6667 Remote Similarity NPC477385
0.6667 Remote Similarity NPC472196
0.6667 Remote Similarity NPC251026
0.6667 Remote Similarity NPC477390
0.6667 Remote Similarity NPC474312
0.6667 Remote Similarity NPC472195
0.6667 Remote Similarity NPC238090
0.6639 Remote Similarity NPC67917
0.6639 Remote Similarity NPC314268
0.6639 Remote Similarity NPC313802
0.6639 Remote Similarity NPC477515
0.6604 Remote Similarity NPC159698
0.6604 Remote Similarity NPC472198
0.6602 Remote Similarity NPC470137
0.66 Remote Similarity NPC38295
0.66 Remote Similarity NPC156089
0.66 Remote Similarity NPC470313
0.66 Remote Similarity NPC473500
0.6596 Remote Similarity NPC132938
0.6579 Remote Similarity NPC133625
0.6571 Remote Similarity NPC208537
0.6571 Remote Similarity NPC270005
0.6566 Remote Similarity NPC82799
0.6562 Remote Similarity NPC326661
0.6559 Remote Similarity NPC474078
0.6556 Remote Similarity NPC477525
0.6538 Remote Similarity NPC285588
0.6535 Remote Similarity NPC314361
0.6532 Remote Similarity NPC314282
0.6514 Remote Similarity NPC313440
0.6509 Remote Similarity NPC320089
0.6509 Remote Similarity NPC320552
0.6505 Remote Similarity NPC125142
0.6495 Remote Similarity NPC110813
0.6484 Remote Similarity NPC315141
0.6484 Remote Similarity NPC78189
0.6484 Remote Similarity NPC129995
0.6476 Remote Similarity NPC473311
0.6476 Remote Similarity NPC327253
0.6471 Remote Similarity NPC6531
0.6465 Remote Similarity NPC100697
0.6449 Remote Similarity NPC470283
0.6444 Remote Similarity NPC13143
0.6444 Remote Similarity NPC294813
0.6442 Remote Similarity NPC248312
0.6442 Remote Similarity NPC316186
0.6435 Remote Similarity NPC473578
0.6429 Remote Similarity NPC316807
0.6429 Remote Similarity NPC133377
0.6423 Remote Similarity NPC315783
0.6423 Remote Similarity NPC314629
0.6422 Remote Similarity NPC240372
0.6415 Remote Similarity NPC110072
0.6415 Remote Similarity NPC302584
0.641 Remote Similarity NPC295444
0.641 Remote Similarity NPC279383
0.641 Remote Similarity NPC268327
0.641 Remote Similarity NPC273215
0.6408 Remote Similarity NPC477387
0.6408 Remote Similarity NPC477389
0.64 Remote Similarity NPC280367
0.6396 Remote Similarity NPC471637
0.6396 Remote Similarity NPC475157
0.6396 Remote Similarity NPC2313
0.6396 Remote Similarity NPC57586
0.6396 Remote Similarity NPC475655
0.6396 Remote Similarity NPC154132
0.6389 Remote Similarity NPC189764
0.6387 Remote Similarity NPC30196
0.6381 Remote Similarity NPC309310
0.6373 Remote Similarity NPC475035
0.6373 Remote Similarity NPC266718
0.6371 Remote Similarity NPC204639
0.6371 Remote Similarity NPC469494
0.6354 Remote Similarity NPC24590
0.6346 Remote Similarity NPC475037
0.6346 Remote Similarity NPC477386
0.6346 Remote Similarity NPC477388
0.6341 Remote Similarity NPC273185
0.6337 Remote Similarity NPC20072
0.6336 Remote Similarity NPC230889
0.633 Remote Similarity NPC90583
0.6328 Remote Similarity NPC475472
0.6316 Remote Similarity NPC472433
0.6316 Remote Similarity NPC315070
0.6306 Remote Similarity NPC64348
0.63 Remote Similarity NPC133226
0.63 Remote Similarity NPC470147
0.6299 Remote Similarity NPC313962
0.6299 Remote Similarity NPC316205
0.6299 Remote Similarity NPC315387
0.6296 Remote Similarity NPC294293
0.6286 Remote Similarity NPC476744
0.6283 Remote Similarity NPC197736
0.6279 Remote Similarity NPC119794
0.6279 Remote Similarity NPC73829
0.6277 Remote Similarity NPC280065
0.6277 Remote Similarity NPC45060
0.6271 Remote Similarity NPC261750
0.6271 Remote Similarity NPC1111
0.626 Remote Similarity NPC472430
0.625 Remote Similarity NPC470836
0.6239 Remote Similarity NPC50902
0.6239 Remote Similarity NPC233273
0.6239 Remote Similarity NPC205546
0.6231 Remote Similarity NPC76999
0.6222 Remote Similarity NPC29468
0.6218 Remote Similarity NPC475988

  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 NPC8098 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
0.9438 High Similarity NPD8522 Clinical (unspecified phase)
0.6964 Remote Similarity NPD6421 Discontinued
0.6842 Remote Similarity NPD6429 Approved
0.6842 Remote Similarity NPD6430 Approved
0.6777 Remote Similarity NPD8341 Approved
0.6777 Remote Similarity NPD8342 Approved
0.6777 Remote Similarity NPD8340 Approved
0.6777 Remote Similarity NPD8299 Approved
0.6727 Remote Similarity NPD1407 Approved
0.6585 Remote Similarity NPD8451 Approved
0.6555 Remote Similarity NPD7641 Discontinued
0.6532 Remote Similarity NPD8448 Approved
0.6529 Remote Similarity NPD8444 Approved
0.646 Remote Similarity NPD5357 Phase 1
0.6423 Remote Similarity NPD7830 Approved
0.6423 Remote Similarity NPD7829 Approved
0.6378 Remote Similarity NPD8392 Approved
0.6378 Remote Similarity NPD8390 Approved
0.6378 Remote Similarity NPD8391 Approved
0.6341 Remote Similarity NPD6436 Phase 3
0.6316 Remote Similarity NPD6640 Phase 3
0.627 Remote Similarity NPD8074 Phase 3
0.6216 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6198 Remote Similarity NPD7505 Discontinued
0.6182 Remote Similarity NPD7839 Suspended
0.6111 Remote Similarity NPD7983 Approved
0.6105 Remote Similarity NPD9445 Approved
0.6034 Remote Similarity NPD4211 Phase 1
0.6032 Remote Similarity NPD7642 Approved
0.6019 Remote Similarity NPD7838 Discovery
0.5938 Remote Similarity NPD8273 Phase 1
0.5935 Remote Similarity NPD7500 Approved
0.5935 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5926 Remote Similarity NPD3716 Discontinued
0.5917 Remote Similarity NPD7116 Clinical (unspecified phase)
0.5893 Remote Similarity NPD6428 Approved
0.5888 Remote Similarity NPD4759 Clinical (unspecified phase)
0.582 Remote Similarity NPD3731 Phase 3
0.5806 Remote Similarity NPD3210 Clinical (unspecified phase)
0.5804 Remote Similarity NPD5381 Approved
0.5804 Remote Similarity NPD5377 Approved
0.5804 Remote Similarity NPD5378 Approved
0.5798 Remote Similarity NPD8174 Phase 2
0.5758 Remote Similarity NPD6914 Discontinued
0.5748 Remote Similarity NPD8513 Phase 3
0.5748 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5748 Remote Similarity NPD8516 Approved
0.5748 Remote Similarity NPD8515 Approved
0.5748 Remote Similarity NPD8517 Approved
0.5727 Remote Similarity NPD3168 Discontinued
0.5727 Remote Similarity NPD46 Approved
0.5727 Remote Similarity NPD6698 Approved
0.5726 Remote Similarity NPD4830 Approved
0.5726 Remote Similarity NPD4832 Approved
0.5726 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5726 Remote Similarity NPD4831 Approved
0.5703 Remote Similarity NPD8080 Discontinued
0.5703 Remote Similarity NPD7623 Phase 3
0.5703 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5667 Remote Similarity NPD6686 Approved
0.5662 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5656 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5649 Remote Similarity NPD7747 Phase 1
0.5649 Remote Similarity NPD7746 Phase 1
0.563 Remote Similarity NPD5376 Approved
0.562 Remote Similarity NPD8305 Approved
0.562 Remote Similarity NPD8306 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