Structure

Physi-Chem Properties

Molecular Weight:  797.64
Volume:  877.815
LogP:  9.899
LogD:  5.239
LogS:  -1.807
# Rotatable Bonds:  39
TPSA:  168.94
# H-Bond Aceptor:  10
# H-Bond Donor:  7
# Rings:  1
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.024
Synthetic Accessibility Score:  4.832
Fsp3:  0.891
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:  -5.478
MDCK Permeability:  3.2165478387469193e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.202
Human Intestinal Absorption (HIA):  0.818
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.004
Plasma Protein Binding (PPB):  101.38927459716797%
Volume Distribution (VD):  0.776
Pgp-substrate:  1.3317224979400635%

ADMET: Metabolism

CYP1A2-inhibitor:  0.013
CYP1A2-substrate:  0.103
CYP2C19-inhibitor:  0.097
CYP2C19-substrate:  0.032
CYP2C9-inhibitor:  0.044
CYP2C9-substrate:  0.995
CYP2D6-inhibitor:  0.033
CYP2D6-substrate:  0.02
CYP3A4-inhibitor:  0.153
CYP3A4-substrate:  0.003

ADMET: Excretion

Clearance (CL):  2.097
Half-life (T1/2):  0.271

ADMET: Toxicity

hERG Blockers:  0.482
Human Hepatotoxicity (H-HT):  0.102
Drug-inuced Liver Injury (DILI):  0.007
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.02
Maximum Recommended Daily Dose:  0.036
Skin Sensitization:  0.97
Carcinogencity:  0.005
Eye Corrosion:  0.003
Eye Irritation:  0.014
Respiratory Toxicity:  0.661

Download Data

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

  Natural Product: NPC15851

Natural Product ID:  NPC15851
Common Name*:   (2S,3R,4E,8E,2'r)-1-O-(Beta-Glucopyranosyl)-N-(2'-Hydroxytetracosanoyl)-4,8-Sphingadienine
IUPAC Name:   (2R)-2-hydroxy-N-[(2S,3R,4E,8E)-3-hydroxy-1-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyhexadeca-4,8-dien-2-yl]tetracosanamide
Synonyms:  
Standard InCHIKey:  YZFYXQFXFONLCR-DSFCUWQCSA-N
Standard InCHI:  InChI=1S/C46H87NO9/c1-3-5-7-9-11-13-15-16-17-18-19-20-21-22-23-25-27-29-31-33-35-40(50)45(54)47-38(37-55-46-44(53)43(52)42(51)41(36-48)56-46)39(49)34-32-30-28-26-24-14-12-10-8-6-4-2/h24,26,32,34,38-44,46,48-53H,3-23,25,27-31,33,35-37H2,1-2H3,(H,47,54)/b26-24+,34-32+/t38-,39+,40+,41+,42+,43-,44+,46+/m0/s1
SMILES:  CCCCCCCCCCCCCCCCCCCCCC[C@H](C(=N[C@H]([C@@H](/C=C/CC/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:   CHEMBL230869
PubChem CID:   16757500
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001766] Fatty acyl glycosides
          • [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

*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
NPO2438 Euryale ferox Species Nymphaeaceae Eukaryota seeds n.a. n.a. PMID[17567070]
NPO2438 Euryale ferox Species Nymphaeaceae Eukaryota n.a. seed n.a. PMID[21280632]
NPO2438 Euryale ferox Species Nymphaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2438 Euryale ferox Species Nymphaeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2438 Euryale ferox Species Nymphaeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2438 Euryale ferox Species Nymphaeaceae 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
NPT140 Organism Artemia Artemia LC50 = 200000.0 nM PMID[478612]

☑ 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 NPC15851 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 NPC309898
1.0 High Similarity NPC263545
1.0 High Similarity NPC473604
1.0 High Similarity NPC111567
1.0 High Similarity NPC475125
1.0 High Similarity NPC473581
1.0 High Similarity NPC186840
1.0 High Similarity NPC473950
0.9882 High Similarity NPC74672
0.9882 High Similarity NPC242503
0.9882 High Similarity NPC43074
0.9882 High Similarity NPC209047
0.9882 High Similarity NPC139782
0.977 High Similarity NPC3568
0.977 High Similarity NPC158445
0.977 High Similarity NPC54961
0.977 High Similarity NPC192066
0.977 High Similarity NPC157353
0.977 High Similarity NPC282088
0.977 High Similarity NPC17290
0.977 High Similarity NPC256570
0.977 High Similarity NPC156782
0.9767 High Similarity NPC182632
0.9767 High Similarity NPC282705
0.9551 High Similarity NPC183449
0.9551 High Similarity NPC197294
0.9551 High Similarity NPC8098
0.9545 High Similarity NPC35269
0.9545 High Similarity NPC70323
0.9545 High Similarity NPC262312
0.9545 High Similarity NPC23454
0.9333 High Similarity NPC45313
0.9318 High Similarity NPC475603
0.9318 High Similarity NPC61894
0.8571 High Similarity NPC201128
0.8454 Intermediate Similarity NPC477198
0.8 Intermediate Similarity NPC288086
0.7843 Intermediate Similarity NPC475918
0.7576 Intermediate Similarity NPC475503
0.7529 Intermediate Similarity NPC291196
0.7529 Intermediate Similarity NPC103712
0.7527 Intermediate Similarity NPC476523
0.75 Intermediate Similarity NPC217095
0.75 Intermediate Similarity NPC264417
0.75 Intermediate Similarity NPC475646
0.7471 Intermediate Similarity NPC55652
0.7404 Intermediate Similarity NPC74035
0.732 Intermediate Similarity NPC39290
0.732 Intermediate Similarity NPC159369
0.7234 Intermediate Similarity NPC228638
0.7156 Intermediate Similarity NPC29501
0.7065 Intermediate Similarity NPC474833
0.7059 Intermediate Similarity NPC189629
0.7021 Intermediate Similarity NPC21693
0.7021 Intermediate Similarity NPC236649
0.7021 Intermediate Similarity NPC469469
0.7019 Intermediate Similarity NPC206711
0.7019 Intermediate Similarity NPC255175
0.7019 Intermediate Similarity NPC225978
0.7019 Intermediate Similarity NPC271207
0.701 Intermediate Similarity NPC208473
0.7 Intermediate Similarity NPC472174
0.6983 Remote Similarity NPC469943
0.6981 Remote Similarity NPC55336
0.6947 Remote Similarity NPC474312
0.6889 Remote Similarity NPC132938
0.6875 Remote Similarity NPC156089
0.6875 Remote Similarity NPC470313
0.6875 Remote Similarity NPC473500
0.6875 Remote Similarity NPC38295
0.6869 Remote Similarity NPC470284
0.6854 Remote Similarity NPC474078
0.6848 Remote Similarity NPC229655
0.6848 Remote Similarity NPC326661
0.6842 Remote Similarity NPC82799
0.6813 Remote Similarity NPC472173
0.6804 Remote Similarity NPC477199
0.6804 Remote Similarity NPC473308
0.6789 Remote Similarity NPC315426
0.6786 Remote Similarity NPC314306
0.6774 Remote Similarity NPC110813
0.6744 Remote Similarity NPC13143
0.6744 Remote Similarity NPC294813
0.6737 Remote Similarity NPC127295
0.6737 Remote Similarity NPC163362
0.6735 Remote Similarity NPC73166
0.6733 Remote Similarity NPC477866
0.6733 Remote Similarity NPC477865
0.6727 Remote Similarity NPC475150
0.6703 Remote Similarity NPC314678
0.6702 Remote Similarity NPC133377
0.6702 Remote Similarity NPC316807
0.6701 Remote Similarity NPC473315
0.6701 Remote Similarity NPC142111
0.6667 Remote Similarity NPC208537
0.6667 Remote Similarity NPC270005
0.6667 Remote Similarity NPC472197
0.6667 Remote Similarity NPC472199
0.6637 Remote Similarity NPC469865
0.6602 Remote Similarity NPC472196
0.6602 Remote Similarity NPC472195
0.6602 Remote Similarity NPC238090
0.6598 Remote Similarity NPC251026
0.6583 Remote Similarity NPC314512
0.6583 Remote Similarity NPC314451
0.6583 Remote Similarity NPC313342
0.6583 Remote Similarity NPC313333
0.6571 Remote Similarity NPC175614
0.6562 Remote Similarity NPC133226
0.6562 Remote Similarity NPC470147
0.6552 Remote Similarity NPC6531
0.6538 Remote Similarity NPC470283
0.6538 Remote Similarity NPC159698
0.6538 Remote Similarity NPC472198
0.6535 Remote Similarity NPC470137
0.6504 Remote Similarity NPC313962
0.6471 Remote Similarity NPC329003
0.6471 Remote Similarity NPC325550
0.6471 Remote Similarity NPC326524
0.6466 Remote Similarity NPC30196
0.6458 Remote Similarity NPC470149
0.6458 Remote Similarity NPC470148
0.6458 Remote Similarity NPC180725
0.6449 Remote Similarity NPC313440
0.6446 Remote Similarity NPC204639
0.6442 Remote Similarity NPC320089
0.6441 Remote Similarity NPC314268
0.6441 Remote Similarity NPC477515
0.6441 Remote Similarity NPC313802
0.6441 Remote Similarity NPC67917
0.6436 Remote Similarity NPC118077
0.6436 Remote Similarity NPC475186
0.6436 Remote Similarity NPC125142
0.6423 Remote Similarity NPC329919
0.6423 Remote Similarity NPC477793
0.6417 Remote Similarity NPC273185
0.6408 Remote Similarity NPC473311
0.6392 Remote Similarity NPC471420
0.6392 Remote Similarity NPC100697
0.6383 Remote Similarity NPC3094
0.6374 Remote Similarity NPC327753
0.6374 Remote Similarity NPC223174
0.6374 Remote Similarity NPC327486
0.6373 Remote Similarity NPC248312
0.6372 Remote Similarity NPC473578
0.6355 Remote Similarity NPC240372
0.6354 Remote Similarity NPC248775
0.6353 Remote Similarity NPC321030
0.6349 Remote Similarity NPC314361
0.6348 Remote Similarity NPC1111
0.6348 Remote Similarity NPC273215
0.6348 Remote Similarity NPC295444
0.6348 Remote Similarity NPC261750
0.6348 Remote Similarity NPC279383
0.6348 Remote Similarity NPC268327
0.6346 Remote Similarity NPC302584
0.6346 Remote Similarity NPC469410
0.6341 Remote Similarity NPC314282
0.6327 Remote Similarity NPC280367
0.63 Remote Similarity NPC266718
0.63 Remote Similarity NPC192025
0.63 Remote Similarity NPC475035
0.63 Remote Similarity NPC125253
0.63 Remote Similarity NPC253975
0.6275 Remote Similarity NPC475037
0.627 Remote Similarity NPC475472
0.6264 Remote Similarity NPC474812
0.6263 Remote Similarity NPC477390
0.6263 Remote Similarity NPC20072
0.6263 Remote Similarity NPC477385
0.6262 Remote Similarity NPC90583
0.626 Remote Similarity NPC315058
0.625 Remote Similarity NPC474026
0.625 Remote Similarity NPC277570
0.6239 Remote Similarity NPC64348
0.623 Remote Similarity NPC315783
0.6228 Remote Similarity NPC133625
0.622 Remote Similarity NPC73829
0.622 Remote Similarity NPC119794
0.6207 Remote Similarity NPC477763
0.6207 Remote Similarity NPC477757
0.6207 Remote Similarity NPC477753
0.6207 Remote Similarity NPC477762
0.6207 Remote Similarity NPC60432
0.6207 Remote Similarity NPC477750
0.6207 Remote Similarity NPC477755
0.6196 Remote Similarity NPC45060
0.6196 Remote Similarity NPC280065
0.6186 Remote Similarity NPC150557
0.6182 Remote Similarity NPC471637
0.6182 Remote Similarity NPC154127
0.6182 Remote Similarity NPC475157
0.6182 Remote Similarity NPC154132
0.6182 Remote Similarity NPC2313
0.6182 Remote Similarity NPC57586
0.6182 Remote Similarity NPC475655
0.618 Remote Similarity NPC31496
0.6176 Remote Similarity NPC470836
0.6172 Remote Similarity NPC78189
0.6172 Remote Similarity NPC76999

  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 NPC15851 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
0.9882 High Similarity NPD8522 Clinical (unspecified phase)
0.7064 Intermediate Similarity NPD6421 Discontinued
0.6981 Remote Similarity NPD1407 Approved
0.6786 Remote Similarity NPD6430 Approved
0.6786 Remote Similarity NPD6429 Approved
0.6583 Remote Similarity NPD8342 Approved
0.6583 Remote Similarity NPD8340 Approved
0.6583 Remote Similarity NPD8299 Approved
0.6583 Remote Similarity NPD8341 Approved
0.6417 Remote Similarity NPD6436 Phase 3
0.6396 Remote Similarity NPD5357 Phase 1
0.6393 Remote Similarity NPD8451 Approved
0.6374 Remote Similarity NPD9445 Approved
0.6341 Remote Similarity NPD8448 Approved
0.6333 Remote Similarity NPD8444 Approved
0.623 Remote Similarity NPD7829 Approved
0.623 Remote Similarity NPD7830 Approved
0.6218 Remote Similarity NPD7641 Discontinued
0.619 Remote Similarity NPD8391 Approved
0.619 Remote Similarity NPD8392 Approved
0.619 Remote Similarity NPD8390 Approved
0.6154 Remote Similarity NPD3716 Discontinued
0.6111 Remote Similarity NPD6428 Approved
0.6098 Remote Similarity NPD7642 Approved
0.6067 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6019 Remote Similarity NPD5381 Approved
0.6019 Remote Similarity NPD5378 Approved
0.6019 Remote Similarity NPD5377 Approved
0.5965 Remote Similarity NPD6640 Phase 3
0.5965 Remote Similarity NPD4211 Phase 1
0.5962 Remote Similarity NPD4759 Clinical (unspecified phase)
0.5952 Remote Similarity NPD8074 Phase 3
0.5929 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5882 Remote Similarity NPD3731 Phase 3
0.5868 Remote Similarity NPD7505 Discontinued
0.5868 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5862 Remote Similarity NPD8174 Phase 2
0.5856 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5818 Remote Similarity NPD7839 Suspended
0.5789 Remote Similarity NPD3212 Clinical (unspecified phase)
0.5785 Remote Similarity NPD4830 Approved
0.5785 Remote Similarity NPD4831 Approved
0.5785 Remote Similarity NPD4832 Approved
0.5755 Remote Similarity NPD618 Clinical (unspecified phase)
0.5741 Remote Similarity NPD7983 Approved
0.5692 Remote Similarity NPD6914 Discontinued
0.569 Remote Similarity NPD5376 Approved
0.5688 Remote Similarity NPD1446 Phase 3
0.5688 Remote Similarity NPD1447 Phase 3
0.568 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5678 Remote Similarity NPD8306 Approved
0.5678 Remote Similarity NPD6941 Approved
0.5678 Remote Similarity NPD8305 Approved
0.5648 Remote Similarity NPD3168 Discontinued
0.5648 Remote Similarity NPD46 Approved
0.5648 Remote Similarity NPD6698 Approved
0.5648 Remote Similarity NPD7838 Discovery
0.5647 Remote Similarity NPD2269 Approved
0.5635 Remote Similarity NPD8080 Discontinued
0.5625 Remote Similarity NPD8273 Phase 1
0.561 Remote Similarity NPD7500 Approved
0.56 Remote Similarity NPD9435 Approved
0.56 Remote Similarity NPD9434 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