Structure

Physi-Chem Properties

Molecular Weight:  535.5
Volume:  626.078
LogP:  9.958
LogD:  5.262
LogS:  -3.16
# Rotatable Bonds:  30
TPSA:  69.56
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.066
Synthetic Accessibility Score:  3.451
Fsp3:  0.853
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Rejected
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:  -5.212
MDCK Permeability:  1.3236822269391268e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.606
Human Intestinal Absorption (HIA):  0.145
20% Bioavailability (F20%):  0.927
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.004
Plasma Protein Binding (PPB):  99.56958770751953%
Volume Distribution (VD):  2.467
Pgp-substrate:  1.0928454399108887%

ADMET: Metabolism

CYP1A2-inhibitor:  0.054
CYP1A2-substrate:  0.163
CYP2C19-inhibitor:  0.164
CYP2C19-substrate:  0.04
CYP2C9-inhibitor:  0.077
CYP2C9-substrate:  0.99
CYP2D6-inhibitor:  0.453
CYP2D6-substrate:  0.061
CYP3A4-inhibitor:  0.34
CYP3A4-substrate:  0.016

ADMET: Excretion

Clearance (CL):  2.943
Half-life (T1/2):  0.228

ADMET: Toxicity

hERG Blockers:  0.392
Human Hepatotoxicity (H-HT):  0.148
Drug-inuced Liver Injury (DILI):  0.015
AMES Toxicity:  0.002
Rat Oral Acute Toxicity:  0.025
Maximum Recommended Daily Dose:  0.292
Skin Sensitization:  0.965
Carcinogencity:  0.009
Eye Corrosion:  0.004
Eye Irritation:  0.149
Respiratory Toxicity:  0.44

Download Data

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

  Natural Product: NPC103712

Natural Product ID:  NPC103712
Common Name*:   N-[(2S,3R,4E,8E)-1,3-Dihydroxyoctadeca-4,8-Dien-2-Yl]Hexadecanamide
IUPAC Name:   N-[(2S,3R,4E,8E)-1,3-dihydroxyoctadeca-4,8-dien-2-yl]hexadecanamide
Synonyms:  
Standard InCHIKey:  GMWIWVUTMCBDSP-ILAZMTIGSA-N
Standard InCHI:  InChI=1S/C34H65NO3/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-33(37)32(31-36)35-34(38)30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h19,21,27,29,32-33,36-37H,3-18,20,22-26,28,30-31H2,1-2H3,(H,35,38)/b21-19+,29-27+/t32-,33+/m0/s1
SMILES:  CCCCCCCCC/C=C/CC/C=C/[C@H]([C@H](CO)N=C(CCCCCCCCCCCCCCC)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL37460
PubChem CID:   14331917
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000257] Sphingolipids
        • [CHEMONTID:0001418] Ceramides
          • [CHEMONTID:0001669] Long-chain ceramides

*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
NPO19125 Hoppea dichotoma Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)84903-1]
NPO19125 Hoppea dichotoma Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[11190384]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. fruit n.a. PMID[16417304]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. branch n.a. PMID[17202693]
NPO17716 Calendula arvensis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[1965654]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17716 Calendula arvensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7783 Agathosma affinis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18846 Gastrolobium grandiflorum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11591 Rhododendron simiarum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18705 Sinularia crassa Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15604 Bombax oleagineum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16964 Aplophyllum tenue n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18376 Oryctolagus cuniculus Species Leporidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16826 Streptomyces refuineus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO15968 Annella mollis Species Subergorgiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17716 Calendula arvensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1307 Rabdosia trichocarpa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18789 Cosmos caudatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16097 Ottonia corcovadensis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO10708 Colchicum kesselringii Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19125 Hoppea dichotoma Species Gentianaceae 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
NPT910 Individual Protein Cholesteryl ester transfer protein Homo sapiens IC50 = 46800.0 nM PMID[521234]

☑ 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 NPC103712 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 NPC291196
0.9412 High Similarity NPC288086
0.8594 High Similarity NPC329003
0.8594 High Similarity NPC326524
0.8594 High Similarity NPC325550
0.8533 High Similarity NPC82799
0.8472 Intermediate Similarity NPC264417
0.8472 Intermediate Similarity NPC217095
0.8438 Intermediate Similarity NPC321030
0.806 Intermediate Similarity NPC29468
0.7971 Intermediate Similarity NPC477525
0.7969 Intermediate Similarity NPC242930
0.7941 Intermediate Similarity NPC55068
0.791 Intermediate Similarity NPC130807
0.7703 Intermediate Similarity NPC314678
0.7619 Intermediate Similarity NPC209047
0.7619 Intermediate Similarity NPC74672
0.7619 Intermediate Similarity NPC242503
0.7619 Intermediate Similarity NPC139782
0.7619 Intermediate Similarity NPC43074
0.7531 Intermediate Similarity NPC477199
0.7529 Intermediate Similarity NPC111567
0.7529 Intermediate Similarity NPC263545
0.7529 Intermediate Similarity NPC473581
0.7529 Intermediate Similarity NPC475125
0.7529 Intermediate Similarity NPC15851
0.7529 Intermediate Similarity NPC186840
0.7529 Intermediate Similarity NPC473950
0.7529 Intermediate Similarity NPC309898
0.7529 Intermediate Similarity NPC473604
0.75 Intermediate Similarity NPC474312
0.7429 Intermediate Similarity NPC471023
0.7429 Intermediate Similarity NPC316674
0.7361 Intermediate Similarity NPC113224
0.7361 Intermediate Similarity NPC129995
0.7361 Intermediate Similarity NPC315141
0.7356 Intermediate Similarity NPC3568
0.7356 Intermediate Similarity NPC256570
0.7356 Intermediate Similarity NPC282088
0.7356 Intermediate Similarity NPC157353
0.7356 Intermediate Similarity NPC17290
0.7356 Intermediate Similarity NPC54961
0.7356 Intermediate Similarity NPC156782
0.7356 Intermediate Similarity NPC192066
0.7356 Intermediate Similarity NPC158445
0.7326 Intermediate Similarity NPC182632
0.7326 Intermediate Similarity NPC282705
0.7286 Intermediate Similarity NPC47333
0.7246 Intermediate Similarity NPC312826
0.7215 Intermediate Similarity NPC474833
0.72 Intermediate Similarity NPC324638
0.7195 Intermediate Similarity NPC228638
0.7191 Intermediate Similarity NPC197294
0.7191 Intermediate Similarity NPC183449
0.7191 Intermediate Similarity NPC8098
0.7183 Intermediate Similarity NPC477106
0.7162 Intermediate Similarity NPC474812
0.7159 Intermediate Similarity NPC262312
0.7159 Intermediate Similarity NPC23454
0.7159 Intermediate Similarity NPC35269
0.7159 Intermediate Similarity NPC70323
0.7121 Intermediate Similarity NPC474496
0.7121 Intermediate Similarity NPC270041
0.7093 Intermediate Similarity NPC39290
0.7093 Intermediate Similarity NPC159369
0.7067 Intermediate Similarity NPC280065
0.7067 Intermediate Similarity NPC45060
0.7059 Intermediate Similarity NPC473847
0.7059 Intermediate Similarity NPC470967
0.7059 Intermediate Similarity NPC471960
0.7059 Intermediate Similarity NPC470969
0.7059 Intermediate Similarity NPC477661
0.7059 Intermediate Similarity NPC475384
0.7059 Intermediate Similarity NPC161838
0.7059 Intermediate Similarity NPC470966
0.7059 Intermediate Similarity NPC470968
0.7015 Intermediate Similarity NPC49059
0.7015 Intermediate Similarity NPC256209
0.7 Intermediate Similarity NPC45313
0.6977 Remote Similarity NPC316186
0.697 Remote Similarity NPC188341
0.697 Remote Similarity NPC49494
0.6957 Remote Similarity NPC470970
0.6933 Remote Similarity NPC249713
0.6932 Remote Similarity NPC61894
0.6932 Remote Similarity NPC475603
0.6912 Remote Similarity NPC473725
0.6912 Remote Similarity NPC477726
0.6912 Remote Similarity NPC473721
0.6912 Remote Similarity NPC477725
0.6912 Remote Similarity NPC473910
0.6912 Remote Similarity NPC473896
0.6912 Remote Similarity NPC475353
0.6912 Remote Similarity NPC473735
0.6857 Remote Similarity NPC325734
0.6849 Remote Similarity NPC235311
0.6849 Remote Similarity NPC253468
0.6842 Remote Similarity NPC471022
0.6835 Remote Similarity NPC3094
0.6835 Remote Similarity NPC476924
0.6818 Remote Similarity NPC473672
0.6818 Remote Similarity NPC261571
0.6818 Remote Similarity NPC474495
0.6813 Remote Similarity NPC475503
0.6812 Remote Similarity NPC261158
0.6812 Remote Similarity NPC24216
0.6812 Remote Similarity NPC306420
0.6812 Remote Similarity NPC104138
0.6806 Remote Similarity NPC145627
0.6765 Remote Similarity NPC473532
0.6761 Remote Similarity NPC150505
0.6761 Remote Similarity NPC74617
0.6739 Remote Similarity NPC475646
0.6719 Remote Similarity NPC319709
0.6719 Remote Similarity NPC289484
0.6714 Remote Similarity NPC168308
0.6714 Remote Similarity NPC302569
0.6667 Remote Similarity NPC273023
0.6667 Remote Similarity NPC297020
0.6625 Remote Similarity NPC62293
0.6625 Remote Similarity NPC140327
0.6625 Remote Similarity NPC212008
0.6625 Remote Similarity NPC51055
0.6618 Remote Similarity NPC187361
0.6618 Remote Similarity NPC477724
0.6618 Remote Similarity NPC26102
0.6591 Remote Similarity NPC34754
0.6582 Remote Similarity NPC305223
0.6567 Remote Similarity NPC151782
0.6567 Remote Similarity NPC129263
0.6562 Remote Similarity NPC76976
0.6528 Remote Similarity NPC122239
0.6522 Remote Similarity NPC110732
0.6522 Remote Similarity NPC132669
0.6522 Remote Similarity NPC269800
0.6522 Remote Similarity NPC184014
0.6522 Remote Similarity NPC246519
0.6522 Remote Similarity NPC44193
0.6522 Remote Similarity NPC14234
0.6495 Remote Similarity NPC74035
0.6486 Remote Similarity NPC470965
0.6471 Remote Similarity NPC39966
0.6429 Remote Similarity NPC201128
0.6429 Remote Similarity NPC79367
0.6418 Remote Similarity NPC72699
0.6389 Remote Similarity NPC226848
0.6386 Remote Similarity NPC473972
0.6386 Remote Similarity NPC473971
0.6386 Remote Similarity NPC475363
0.6377 Remote Similarity NPC34577
0.6377 Remote Similarity NPC303672
0.6364 Remote Similarity NPC470663
0.6364 Remote Similarity NPC195165
0.6351 Remote Similarity NPC475984
0.6324 Remote Similarity NPC89824
0.6324 Remote Similarity NPC471959
0.6324 Remote Similarity NPC71053
0.6324 Remote Similarity NPC329608
0.6324 Remote Similarity NPC477723
0.6324 Remote Similarity NPC256656
0.6324 Remote Similarity NPC294278
0.6324 Remote Similarity NPC197272
0.6324 Remote Similarity NPC165447
0.6324 Remote Similarity NPC76198
0.6324 Remote Similarity NPC224148
0.6324 Remote Similarity NPC475477
0.6324 Remote Similarity NPC9273
0.6324 Remote Similarity NPC59408
0.6324 Remote Similarity NPC170776
0.6316 Remote Similarity NPC136164
0.6316 Remote Similarity NPC308844
0.6316 Remote Similarity NPC245947
0.6316 Remote Similarity NPC255863
0.6301 Remote Similarity NPC475931
0.6289 Remote Similarity NPC477198
0.6282 Remote Similarity NPC23721
0.6279 Remote Similarity NPC224072
0.6279 Remote Similarity NPC469838
0.6279 Remote Similarity NPC469833
0.6277 Remote Similarity NPC175614
0.6269 Remote Similarity NPC248884
0.6269 Remote Similarity NPC85079
0.6269 Remote Similarity NPC31194
0.6269 Remote Similarity NPC153538
0.6267 Remote Similarity NPC182758
0.6267 Remote Similarity NPC29697
0.625 Remote Similarity NPC252978
0.6237 Remote Similarity NPC473314
0.6235 Remote Similarity NPC207657
0.6234 Remote Similarity NPC187315
0.6232 Remote Similarity NPC195986
0.6216 Remote Similarity NPC6795
0.6216 Remote Similarity NPC327112
0.6203 Remote Similarity NPC127145
0.6203 Remote Similarity NPC470436
0.6203 Remote Similarity NPC475930
0.6197 Remote Similarity NPC317899
0.6197 Remote Similarity NPC471992
0.6196 Remote Similarity NPC319473
0.6184 Remote Similarity NPC470320

  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 NPC103712 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
0.7941 Intermediate Similarity NPD3210 Clinical (unspecified phase)
0.7619 Intermediate Similarity NPD8522 Clinical (unspecified phase)
0.72 Intermediate Similarity NPD3212 Clinical (unspecified phase)
0.6719 Remote Similarity NPD3211 Approved
0.6351 Remote Similarity NPD6949 Clinical (unspecified phase)
0.6216 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6105 Remote Similarity NPD4228 Discovery
0.6061 Remote Similarity NPD1152 Phase 2
0.6061 Remote Similarity NPD4265 Approved
0.6019 Remote Similarity NPD6421 Discontinued
0.6 Remote Similarity NPD3215 Phase 1
0.5957 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5922 Remote Similarity NPD6413 Approved
0.5914 Remote Similarity NPD6095 Approved
0.5914 Remote Similarity NPD6094 Approved
0.5865 Remote Similarity NPD6420 Discontinued
0.5854 Remote Similarity NPD3187 Discontinued
0.5825 Remote Similarity NPD6406 Approved
0.5769 Remote Similarity NPD3197 Phase 1
0.5765 Remote Similarity NPD818 Approved
0.5765 Remote Similarity NPD819 Approved
0.5729 Remote Similarity NPD5771 Approved
0.5714 Remote Similarity NPD3214 Discontinued
0.567 Remote Similarity NPD4814 Discontinued
0.5647 Remote Similarity NPD8264 Approved
0.5632 Remote Similarity NPD4268 Approved
0.5632 Remote Similarity NPD4271 Approved
0.5632 Remote Similarity NPD3732 Approved
0.5631 Remote Similarity NPD5357 Phase 1
0.5631 Remote Similarity NPD6640 Phase 3
0.561 Remote Similarity NPD15 Approved
0.561 Remote Similarity NPD1082 Approved
0.561 Remote Similarity NPD791 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