Structure

Physi-Chem Properties

Molecular Weight:  795.62
Volume:  875.178
LogP:  8.413
LogD:  4.85
LogS:  -1.833
# Rotatable Bonds:  38
TPSA:  168.94
# H-Bond Aceptor:  10
# H-Bond Donor:  7
# Rings:  1
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.019
Synthetic Accessibility Score:  4.927
Fsp3:  0.848
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:  -5.435
MDCK Permeability:  9.681387382443063e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.103
Human Intestinal Absorption (HIA):  0.725
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.004
Plasma Protein Binding (PPB):  100.22718048095703%
Volume Distribution (VD):  0.897
Pgp-substrate:  1.8139935731887817%

ADMET: Metabolism

CYP1A2-inhibitor:  0.02
CYP1A2-substrate:  0.113
CYP2C19-inhibitor:  0.165
CYP2C19-substrate:  0.04
CYP2C9-inhibitor:  0.086
CYP2C9-substrate:  0.998
CYP2D6-inhibitor:  0.123
CYP2D6-substrate:  0.153
CYP3A4-inhibitor:  0.273
CYP3A4-substrate:  0.008

ADMET: Excretion

Clearance (CL):  1.628
Half-life (T1/2):  0.17

ADMET: Toxicity

hERG Blockers:  0.835
Human Hepatotoxicity (H-HT):  0.082
Drug-inuced Liver Injury (DILI):  0.012
AMES Toxicity:  0.064
Rat Oral Acute Toxicity:  0.018
Maximum Recommended Daily Dose:  0.023
Skin Sensitization:  0.97
Carcinogencity:  0.009
Eye Corrosion:  0.003
Eye Irritation:  0.014
Respiratory Toxicity:  0.523

Download Data

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

  Natural Product: NPC156782

Natural Product ID:  NPC156782
Common Name*:   Renieroside A4
IUPAC Name:   (2R)-2-hydroxy-N-[(2S,3R,4E,8E,10E)-3-hydroxy-1-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoctadeca-4,8,10-trien-2-yl]docosanamide
Synonyms:   renieroside A4
Standard InCHIKey:  XESDOPMJHRNWTH-KEJMQFMQSA-N
Standard InCHI:  InChI=1S/C46H85NO9/c1-3-5-7-9-11-13-15-17-18-19-20-21-23-25-27-29-31-33-35-40(50)45(54)47-38(37-55-46-44(53)43(52)42(51)41(36-48)56-46)39(49)34-32-30-28-26-24-22-16-14-12-10-8-6-4-2/h16,22,24,26,32,34,38-44,46,48-53H,3-15,17-21,23,25,27-31,33,35-37H2,1-2H3,(H,47,54)/b22-16+,26-24+,34-32+/t38-,39+,40+,41+,42+,43-,44+,46+/m0/s1
SMILES:  CCCCCCCCCCCCCCCCCCCC[C@H](C(=N[C@H]([C@@H](/C=C/CC/C=C/C=C/CCCCCCC)O)CO[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL219746
PubChem CID:   23643540
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[525335]
NPT146 Cell Line SK-OV-3 Homo sapiens ED50 > 10.0 ug ml-1 PMID[525335]
NPT147 Cell Line SK-MEL-2 Homo sapiens ED50 > 10.0 ug ml-1 PMID[525335]
NPT574 Cell Line XF498 Homo sapiens ED50 > 10.0 ug ml-1 PMID[525335]
NPT148 Cell Line HCT-15 Homo sapiens ED50 > 10.0 ug ml-1 PMID[525335]

☑ 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 NPC156782 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 NPC158445
1.0 High Similarity NPC157353
1.0 High Similarity NPC282088
1.0 High Similarity NPC54961
0.9775 High Similarity NPC8098
0.9775 High Similarity NPC183449
0.9775 High Similarity NPC197294
0.977 High Similarity NPC473950
0.977 High Similarity NPC473604
0.977 High Similarity NPC473581
0.977 High Similarity NPC475125
0.977 High Similarity NPC111567
0.977 High Similarity NPC263545
0.977 High Similarity NPC186840
0.977 High Similarity NPC309898
0.977 High Similarity NPC15851
0.9655 High Similarity NPC209047
0.9655 High Similarity NPC139782
0.9655 High Similarity NPC242503
0.9655 High Similarity NPC43074
0.9655 High Similarity NPC74672
0.9556 High Similarity NPC45313
0.9551 High Similarity NPC17290
0.9551 High Similarity NPC192066
0.9551 High Similarity NPC3568
0.9551 High Similarity NPC256570
0.9545 High Similarity NPC182632
0.9545 High Similarity NPC282705
0.9333 High Similarity NPC23454
0.9333 High Similarity NPC35269
0.9333 High Similarity NPC262312
0.9333 High Similarity NPC70323
0.9111 High Similarity NPC475603
0.9111 High Similarity NPC61894
0.84 Intermediate Similarity NPC201128
0.8283 Intermediate Similarity NPC477198
0.7816 Intermediate Similarity NPC288086
0.7692 Intermediate Similarity NPC475918
0.7426 Intermediate Similarity NPC475503
0.7368 Intermediate Similarity NPC476523
0.7356 Intermediate Similarity NPC291196
0.7356 Intermediate Similarity NPC103712
0.7353 Intermediate Similarity NPC475646
0.7339 Intermediate Similarity NPC29501
0.7333 Intermediate Similarity NPC217095
0.7333 Intermediate Similarity NPC264417
0.7303 Intermediate Similarity NPC55652
0.7264 Intermediate Similarity NPC74035
0.7216 Intermediate Similarity NPC208473
0.7172 Intermediate Similarity NPC159369
0.7172 Intermediate Similarity NPC39290
0.717 Intermediate Similarity NPC55336
0.7083 Intermediate Similarity NPC228638
0.7033 Intermediate Similarity NPC472173
0.701 Intermediate Similarity NPC473308
0.6972 Remote Similarity NPC315426
0.6931 Remote Similarity NPC477865
0.6931 Remote Similarity NPC477866
0.6923 Remote Similarity NPC314678
0.6923 Remote Similarity NPC189629
0.6915 Remote Similarity NPC474833
0.6907 Remote Similarity NPC473315
0.6907 Remote Similarity NPC142111
0.6887 Remote Similarity NPC255175
0.6887 Remote Similarity NPC271207
0.6887 Remote Similarity NPC225978
0.6887 Remote Similarity NPC206711
0.6875 Remote Similarity NPC236649
0.6875 Remote Similarity NPC21693
0.6875 Remote Similarity NPC469469
0.6864 Remote Similarity NPC469943
0.6848 Remote Similarity NPC472174
0.6804 Remote Similarity NPC474312
0.6804 Remote Similarity NPC251026
0.6762 Remote Similarity NPC175614
0.675 Remote Similarity NPC314451
0.675 Remote Similarity NPC313342
0.675 Remote Similarity NPC314512
0.675 Remote Similarity NPC313333
0.6739 Remote Similarity NPC132938
0.6735 Remote Similarity NPC473500
0.6735 Remote Similarity NPC156089
0.6735 Remote Similarity NPC470313
0.6735 Remote Similarity NPC38295
0.6733 Remote Similarity NPC470284
0.6733 Remote Similarity NPC470137
0.6703 Remote Similarity NPC474078
0.6702 Remote Similarity NPC326661
0.6702 Remote Similarity NPC229655
0.6701 Remote Similarity NPC82799
0.6667 Remote Similarity NPC314306
0.6667 Remote Similarity NPC477199
0.6634 Remote Similarity NPC475186
0.6634 Remote Similarity NPC118077
0.6632 Remote Similarity NPC110813
0.661 Remote Similarity NPC67917
0.661 Remote Similarity NPC477515
0.661 Remote Similarity NPC313802
0.661 Remote Similarity NPC314268
0.6607 Remote Similarity NPC475150
0.6602 Remote Similarity NPC473311
0.66 Remote Similarity NPC73166
0.6598 Remote Similarity NPC127295
0.6598 Remote Similarity NPC163362
0.6591 Remote Similarity NPC13143
0.6591 Remote Similarity NPC294813
0.6585 Remote Similarity NPC329919
0.6585 Remote Similarity NPC477793
0.6562 Remote Similarity NPC133377
0.6562 Remote Similarity NPC316807
0.6538 Remote Similarity NPC472199
0.6538 Remote Similarity NPC208537
0.6538 Remote Similarity NPC270005
0.6538 Remote Similarity NPC472197
0.6522 Remote Similarity NPC469865
0.6508 Remote Similarity NPC314361
0.6504 Remote Similarity NPC314282
0.6476 Remote Similarity NPC472196
0.6476 Remote Similarity NPC238090
0.6476 Remote Similarity NPC472195
0.6465 Remote Similarity NPC477390
0.6465 Remote Similarity NPC477385
0.6441 Remote Similarity NPC6531
0.6429 Remote Similarity NPC133226
0.6429 Remote Similarity NPC470147
0.6415 Remote Similarity NPC470283
0.6415 Remote Similarity NPC159698
0.6415 Remote Similarity NPC472198
0.6404 Remote Similarity NPC133625
0.64 Remote Similarity NPC313962
0.6393 Remote Similarity NPC315783
0.6364 Remote Similarity NPC2313
0.6364 Remote Similarity NPC475157
0.6364 Remote Similarity NPC57586
0.6364 Remote Similarity NPC475655
0.6364 Remote Similarity NPC471637
0.6364 Remote Similarity NPC154132
0.6356 Remote Similarity NPC30196
0.6346 Remote Similarity NPC285588
0.6341 Remote Similarity NPC204639
0.6333 Remote Similarity NPC477525
0.633 Remote Similarity NPC313440
0.6328 Remote Similarity NPC78189
0.6327 Remote Similarity NPC470148
0.6327 Remote Similarity NPC470149
0.6327 Remote Similarity NPC180725
0.6322 Remote Similarity NPC326524
0.6322 Remote Similarity NPC329003
0.6322 Remote Similarity NPC325550
0.6321 Remote Similarity NPC320089
0.6321 Remote Similarity NPC320552
0.6311 Remote Similarity NPC273185
0.6311 Remote Similarity NPC125142
0.6286 Remote Similarity NPC327253
0.6283 Remote Similarity NPC315070
0.6264 Remote Similarity NPC315141
0.6264 Remote Similarity NPC129995
0.6263 Remote Similarity NPC471420
0.6263 Remote Similarity NPC100697
0.6261 Remote Similarity NPC473578
0.626 Remote Similarity NPC314629
0.625 Remote Similarity NPC248312
0.625 Remote Similarity NPC316186
0.625 Remote Similarity NPC3094
0.625 Remote Similarity NPC197736
0.6239 Remote Similarity NPC279383
0.6239 Remote Similarity NPC273215
0.6239 Remote Similarity NPC261750
0.6239 Remote Similarity NPC268327
0.6239 Remote Similarity NPC1111
0.6239 Remote Similarity NPC240372
0.6239 Remote Similarity NPC295444
0.6237 Remote Similarity NPC223174
0.6237 Remote Similarity NPC327486
0.6237 Remote Similarity NPC327753
0.6226 Remote Similarity NPC110072
0.6226 Remote Similarity NPC302584
0.6226 Remote Similarity NPC469410
0.6224 Remote Similarity NPC248775
0.6214 Remote Similarity NPC477387
0.6214 Remote Similarity NPC477389
0.621 Remote Similarity NPC469494
0.6207 Remote Similarity NPC321030
0.6204 Remote Similarity NPC189764
0.62 Remote Similarity NPC280367
0.619 Remote Similarity NPC309310
0.6183 Remote Similarity NPC230889
0.6176 Remote Similarity NPC125253
0.6176 Remote Similarity NPC192025
0.6176 Remote Similarity NPC253975
0.6176 Remote Similarity NPC475035
0.6176 Remote Similarity NPC266718
0.6172 Remote Similarity NPC475472
0.6162 Remote Similarity NPC1180
0.616 Remote Similarity NPC315058
0.6154 Remote Similarity NPC475037
0.6154 Remote Similarity NPC477388
0.6154 Remote Similarity NPC477386
0.6148 Remote Similarity NPC314482
0.6147 Remote Similarity NPC90583

  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 NPC156782 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
0.9655 High Similarity NPD8522 Clinical (unspecified phase)
0.6937 Remote Similarity NPD6421 Discontinued
0.6852 Remote Similarity NPD1407 Approved
0.675 Remote Similarity NPD8299 Approved
0.675 Remote Similarity NPD8340 Approved
0.675 Remote Similarity NPD8342 Approved
0.675 Remote Similarity NPD8341 Approved
0.6667 Remote Similarity NPD6430 Approved
0.6667 Remote Similarity NPD6429 Approved
0.6557 Remote Similarity NPD8451 Approved
0.6504 Remote Similarity NPD8448 Approved
0.65 Remote Similarity NPD8444 Approved
0.6393 Remote Similarity NPD7829 Approved
0.6393 Remote Similarity NPD7830 Approved
0.6387 Remote Similarity NPD7641 Discontinued
0.6349 Remote Similarity NPD8391 Approved
0.6349 Remote Similarity NPD8392 Approved
0.6349 Remote Similarity NPD8390 Approved
0.6311 Remote Similarity NPD6436 Phase 3
0.6283 Remote Similarity NPD5357 Phase 1
0.6237 Remote Similarity NPD9445 Approved
0.614 Remote Similarity NPD6640 Phase 3
0.6111 Remote Similarity NPD8074 Phase 3
0.6038 Remote Similarity NPD3716 Discontinued
0.6036 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6033 Remote Similarity NPD7505 Discontinued
0.6 Remote Similarity NPD6428 Approved
0.6 Remote Similarity NPD7839 Suspended
0.6 Remote Similarity NPD7642 Approved
0.5934 Remote Similarity NPD3210 Clinical (unspecified phase)
0.5926 Remote Similarity NPD7983 Approved
0.5909 Remote Similarity NPD5381 Approved
0.5909 Remote Similarity NPD5378 Approved
0.5909 Remote Similarity NPD5377 Approved
0.5862 Remote Similarity NPD4211 Phase 1
0.5849 Remote Similarity NPD4759 Clinical (unspecified phase)
0.5833 Remote Similarity NPD7838 Discovery
0.5826 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5785 Remote Similarity NPD3731 Phase 3
0.5781 Remote Similarity NPD8273 Phase 1
0.5772 Remote Similarity NPD7500 Approved
0.5772 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5763 Remote Similarity NPD8174 Phase 2
0.575 Remote Similarity NPD7116 Clinical (unspecified phase)
0.5691 Remote Similarity NPD4832 Approved
0.5691 Remote Similarity NPD4831 Approved
0.5691 Remote Similarity NPD4830 Approved
0.567 Remote Similarity NPD3212 Clinical (unspecified phase)
0.5648 Remote Similarity NPD618 Clinical (unspecified phase)
0.5606 Remote Similarity NPD6914 Discontinued

  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