Structure

Physi-Chem Properties

Molecular Weight:  281.25
Volume:  330.873
LogP:  4.05
LogD:  2.761
LogS:  -3.025
# Rotatable Bonds:  15
TPSA:  40.13
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.32
Synthetic Accessibility Score:  2.547
Fsp3:  0.833
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.859
MDCK Permeability:  2.8231046599103138e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.022
20% Bioavailability (F20%):  0.997
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.049
Plasma Protein Binding (PPB):  98.6480941772461%
Volume Distribution (VD):  0.824
Pgp-substrate:  0.6609356999397278%

ADMET: Metabolism

CYP1A2-inhibitor:  0.355
CYP1A2-substrate:  0.211
CYP2C19-inhibitor:  0.464
CYP2C19-substrate:  0.13
CYP2C9-inhibitor:  0.365
CYP2C9-substrate:  0.988
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.061
CYP3A4-inhibitor:  0.121
CYP3A4-substrate:  0.027

ADMET: Excretion

Clearance (CL):  2.946
Half-life (T1/2):  0.637

ADMET: Toxicity

hERG Blockers:  0.147
Human Hepatotoxicity (H-HT):  0.291
Drug-inuced Liver Injury (DILI):  0.04
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.044
Maximum Recommended Daily Dose:  0.029
Skin Sensitization:  0.954
Carcinogencity:  0.129
Eye Corrosion:  0.942
Eye Irritation:  0.963
Respiratory Toxicity:  0.859

Download Data

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

  Natural Product: NPC262968

Natural Product ID:  NPC262968
Common Name*:   Sodium Oleic Acid
IUPAC Name:   sodium;(Z)-octadec-9-enoate
Synonyms:  
Standard InCHIKey:  BCKXLBQYZLBQEK-KVVVOXFISA-M
Standard InCHI:  InChI=1S/C18H34O2.Na/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20;/h9-10H,2-8,11-17H2,1H3,(H,19,20);/q;+1/p-1/b10-9-;
SMILES:  CCCCCCCC/C=CCCCCCCCC(=O)[O-].[Na+]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3527599
PubChem CID:   23665730
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0002949] Long-chain fatty acids

*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
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. PMID[26562741]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. PMID[29517238]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. PMID[31625751]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. Along the Valencian coast, Spain 2020-Jun&Jul PMID[35161358]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota Herb n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]

☑ 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
NPT5277 Individual Protein Cytochrome P450 1A2 Rattus norvegicus Ki = 16700.0 nM PMID[485984]

☑ 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 NPC262968 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
0.9787 High Similarity NPC224227
0.9592 High Similarity NPC139545
0.9592 High Similarity NPC39633
0.9592 High Similarity NPC309606
0.94 High Similarity NPC6095
0.94 High Similarity NPC88966
0.94 High Similarity NPC154245
0.94 High Similarity NPC290563
0.94 High Similarity NPC261831
0.94 High Similarity NPC25417
0.94 High Similarity NPC85813
0.94 High Similarity NPC32467
0.94 High Similarity NPC281972
0.94 High Similarity NPC87564
0.94 High Similarity NPC424
0.9216 High Similarity NPC228473
0.9216 High Similarity NPC200845
0.9216 High Similarity NPC10316
0.9216 High Similarity NPC223677
0.9216 High Similarity NPC128061
0.9216 High Similarity NPC28779
0.92 High Similarity NPC139029
0.92 High Similarity NPC36061
0.92 High Similarity NPC294548
0.92 High Similarity NPC321062
0.92 High Similarity NPC70387
0.92 High Similarity NPC1813
0.9038 High Similarity NPC18951
0.9038 High Similarity NPC477201
0.9 High Similarity NPC281245
0.9 High Similarity NPC92114
0.8824 High Similarity NPC71761
0.8679 High Similarity NPC187777
0.8679 High Similarity NPC179764
0.86 High Similarity NPC59051
0.8571 High Similarity NPC216130
0.8545 High Similarity NPC274927
0.8545 High Similarity NPC106851
0.8519 High Similarity NPC225929
0.8491 Intermediate Similarity NPC54766
0.8491 Intermediate Similarity NPC274290
0.8491 Intermediate Similarity NPC473863
0.84 Intermediate Similarity NPC149821
0.84 Intermediate Similarity NPC5413
0.8393 Intermediate Similarity NPC243532
0.8393 Intermediate Similarity NPC229252
0.8393 Intermediate Similarity NPC143857
0.8269 Intermediate Similarity NPC161366
0.8246 Intermediate Similarity NPC201939
0.82 Intermediate Similarity NPC180534
0.82 Intermediate Similarity NPC91495
0.82 Intermediate Similarity NPC207292
0.8103 Intermediate Similarity NPC54925
0.807 Intermediate Similarity NPC251042
0.807 Intermediate Similarity NPC174447
0.807 Intermediate Similarity NPC122521
0.807 Intermediate Similarity NPC235242
0.8039 Intermediate Similarity NPC207815
0.7966 Intermediate Similarity NPC328089
0.7966 Intermediate Similarity NPC68343
0.7963 Intermediate Similarity NPC87394
0.7931 Intermediate Similarity NPC40082
0.7931 Intermediate Similarity NPC125312
0.7931 Intermediate Similarity NPC174560
0.7925 Intermediate Similarity NPC18357
0.7833 Intermediate Similarity NPC245947
0.7833 Intermediate Similarity NPC326268
0.7833 Intermediate Similarity NPC136164
0.7833 Intermediate Similarity NPC318420
0.7833 Intermediate Similarity NPC255863
0.78 Intermediate Similarity NPC117572
0.7736 Intermediate Similarity NPC28205
0.7736 Intermediate Similarity NPC284212
0.7736 Intermediate Similarity NPC470412
0.7736 Intermediate Similarity NPC470410
0.7719 Intermediate Similarity NPC267817
0.7719 Intermediate Similarity NPC34416
0.7692 Intermediate Similarity NPC163345
0.7667 Intermediate Similarity NPC470320
0.7647 Intermediate Similarity NPC110234
0.7647 Intermediate Similarity NPC44363
0.7647 Intermediate Similarity NPC163751
0.7627 Intermediate Similarity NPC321838
0.7627 Intermediate Similarity NPC320305
0.7627 Intermediate Similarity NPC328776
0.7593 Intermediate Similarity NPC310746
0.7581 Intermediate Similarity NPC99619
0.7581 Intermediate Similarity NPC475443
0.7581 Intermediate Similarity NPC22101
0.7581 Intermediate Similarity NPC473829
0.7581 Intermediate Similarity NPC148192
0.7581 Intermediate Similarity NPC271921
0.7581 Intermediate Similarity NPC330426
0.7581 Intermediate Similarity NPC104537
0.7581 Intermediate Similarity NPC127091
0.7581 Intermediate Similarity NPC26500
0.75 Intermediate Similarity NPC52264
0.75 Intermediate Similarity NPC477984
0.75 Intermediate Similarity NPC474672
0.746 Intermediate Similarity NPC324981
0.746 Intermediate Similarity NPC141481
0.746 Intermediate Similarity NPC48218
0.746 Intermediate Similarity NPC473559
0.7458 Intermediate Similarity NPC45097
0.7451 Intermediate Similarity NPC239754
0.7407 Intermediate Similarity NPC48162
0.7407 Intermediate Similarity NPC477458
0.74 Intermediate Similarity NPC270796
0.7377 Intermediate Similarity NPC226592
0.7368 Intermediate Similarity NPC325977
0.7344 Intermediate Similarity NPC473772
0.7344 Intermediate Similarity NPC317583
0.7321 Intermediate Similarity NPC137538
0.7273 Intermediate Similarity NPC216407
0.7231 Intermediate Similarity NPC476660
0.7231 Intermediate Similarity NPC42526
0.7213 Intermediate Similarity NPC477707
0.7193 Intermediate Similarity NPC45626
0.7188 Intermediate Similarity NPC218477
0.7188 Intermediate Similarity NPC476614
0.7167 Intermediate Similarity NPC328311
0.7167 Intermediate Similarity NPC327112
0.7143 Intermediate Similarity NPC154728
0.7143 Intermediate Similarity NPC12156
0.7143 Intermediate Similarity NPC304665
0.7143 Intermediate Similarity NPC161097
0.7143 Intermediate Similarity NPC126899
0.7143 Intermediate Similarity NPC28598
0.7119 Intermediate Similarity NPC329819
0.7097 Intermediate Similarity NPC234767
0.7077 Intermediate Similarity NPC143396
0.7049 Intermediate Similarity NPC477829
0.7037 Intermediate Similarity NPC250919
0.7037 Intermediate Similarity NPC98284
0.7031 Intermediate Similarity NPC60120
0.7018 Intermediate Similarity NPC322461
0.7015 Intermediate Similarity NPC474705
0.7015 Intermediate Similarity NPC167145
0.7015 Intermediate Similarity NPC470237
0.7 Intermediate Similarity NPC216630
0.7 Intermediate Similarity NPC149184
0.7 Intermediate Similarity NPC171736
0.7 Intermediate Similarity NPC196924
0.7 Intermediate Similarity NPC329550
0.7 Intermediate Similarity NPC209970
0.7 Intermediate Similarity NPC307783
0.6981 Remote Similarity NPC42304
0.697 Remote Similarity NPC475310
0.6964 Remote Similarity NPC129458
0.6949 Remote Similarity NPC323597
0.6949 Remote Similarity NPC323498
0.6949 Remote Similarity NPC323436
0.6949 Remote Similarity NPC211752
0.6923 Remote Similarity NPC53302
0.6912 Remote Similarity NPC330016
0.6912 Remote Similarity NPC474321
0.6912 Remote Similarity NPC166797
0.6912 Remote Similarity NPC227396
0.6909 Remote Similarity NPC474391
0.6885 Remote Similarity NPC299730
0.6875 Remote Similarity NPC308294
0.6875 Remote Similarity NPC16119
0.6875 Remote Similarity NPC142423
0.6875 Remote Similarity NPC284447
0.6866 Remote Similarity NPC320669
0.6866 Remote Similarity NPC318814
0.6866 Remote Similarity NPC160817
0.6866 Remote Similarity NPC84038
0.6863 Remote Similarity NPC203531
0.6863 Remote Similarity NPC236579
0.6863 Remote Similarity NPC67462
0.6842 Remote Similarity NPC10081
0.6842 Remote Similarity NPC225066
0.6833 Remote Similarity NPC469373
0.6825 Remote Similarity NPC34883
0.6818 Remote Similarity NPC199557
0.6812 Remote Similarity NPC228978
0.6812 Remote Similarity NPC476844
0.6809 Remote Similarity NPC156630
0.6792 Remote Similarity NPC76976
0.6786 Remote Similarity NPC234829
0.678 Remote Similarity NPC327388
0.6769 Remote Similarity NPC474619
0.6765 Remote Similarity NPC325627
0.6735 Remote Similarity NPC22903
0.6735 Remote Similarity NPC305660
0.6735 Remote Similarity NPC92863
0.6735 Remote Similarity NPC201622
0.6735 Remote Similarity NPC54980
0.6735 Remote Similarity NPC155880
0.6731 Remote Similarity NPC74845
0.6731 Remote Similarity NPC317128
0.6721 Remote Similarity NPC329249
0.6721 Remote Similarity NPC474267
0.6719 Remote Similarity NPC323045
0.6719 Remote Similarity NPC320642
0.6719 Remote Similarity NPC476657
0.6719 Remote Similarity NPC317881
0.6719 Remote Similarity NPC98897
0.6719 Remote Similarity NPC476655

  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 NPC262968 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
1.0 High Similarity NPD29 Approved
1.0 High Similarity NPD28 Approved
0.94 High Similarity NPD3194 Approved
0.94 High Similarity NPD3196 Approved
0.94 High Similarity NPD3195 Phase 2
0.94 High Similarity NPD4266 Approved
0.92 High Similarity NPD3172 Approved
0.8936 High Similarity NPD3174 Discontinued
0.84 Intermediate Similarity NPD3173 Approved
0.82 Intermediate Similarity NPD622 Approved
0.7966 Intermediate Similarity NPD3197 Phase 1
0.7843 Intermediate Similarity NPD5343 Approved
0.78 Intermediate Similarity NPD4222 Approved
0.78 Intermediate Similarity NPD39 Approved
0.7447 Intermediate Similarity NPD3206 Approved
0.74 Intermediate Similarity NPD5326 Phase 3
0.7255 Intermediate Similarity NPD6097 Approved
0.7255 Intermediate Similarity NPD6096 Approved
0.7167 Intermediate Similarity NPD4246 Clinical (unspecified phase)
0.7 Intermediate Similarity NPD2270 Approved
0.6875 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6812 Remote Similarity NPD8039 Approved
0.6615 Remote Similarity NPD7331 Phase 2
0.6604 Remote Similarity NPD2699 Approved
0.6604 Remote Similarity NPD3199 Clinical (unspecified phase)
0.66 Remote Similarity NPD633 Phase 3
0.66 Remote Similarity NPD9448 Phase 2
0.6528 Remote Similarity NPD3732 Approved
0.6515 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6491 Remote Similarity NPD6927 Phase 3
0.6406 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6351 Remote Similarity NPD5368 Approved
0.6301 Remote Similarity NPD5784 Clinical (unspecified phase)
0.629 Remote Similarity NPD6109 Phase 1
0.6275 Remote Similarity NPD9655 Approved
0.6275 Remote Similarity NPD5783 Phase 3
0.6267 Remote Similarity NPD5369 Approved
0.6226 Remote Similarity NPD387 Clinical (unspecified phase)
0.6184 Remote Similarity NPD6435 Approved
0.6184 Remote Similarity NPD4269 Approved
0.6184 Remote Similarity NPD4270 Approved
0.6164 Remote Similarity NPD4756 Discovery
0.6133 Remote Similarity NPD4252 Approved
0.6104 Remote Similarity NPD7154 Phase 3
0.6104 Remote Similarity NPD5362 Discontinued
0.6081 Remote Similarity NPD4268 Approved
0.6081 Remote Similarity NPD4271 Approved
0.597 Remote Similarity NPD7341 Phase 2
0.5965 Remote Similarity NPD6125 Clinical (unspecified phase)
0.5949 Remote Similarity NPD5363 Approved
0.5921 Remote Similarity NPD4819 Approved
0.5921 Remote Similarity NPD4820 Approved
0.5921 Remote Similarity NPD4821 Approved
0.5921 Remote Similarity NPD4822 Approved
0.5921 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5893 Remote Similarity NPD634 Phase 3
0.5875 Remote Similarity NPD5786 Approved
0.5862 Remote Similarity NPD4220 Pre-registration
0.5833 Remote Similarity NPD3186 Phase 1
0.5769 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5735 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5696 Remote Similarity NPD5332 Approved
0.5696 Remote Similarity NPD5331 Approved
0.5679 Remote Similarity NPD6422 Discontinued
0.5679 Remote Similarity NPD6409 Approved
0.5679 Remote Similarity NPD7146 Approved
0.5679 Remote Similarity NPD5330 Approved
0.5679 Remote Similarity NPD7521 Approved
0.5679 Remote Similarity NPD7334 Approved
0.5679 Remote Similarity NPD6684 Approved
0.5679 Remote Similarity NPD6098 Approved
0.5663 Remote Similarity NPD5347 Phase 2
0.5663 Remote Similarity NPD6101 Approved
0.5663 Remote Similarity NPD5346 Phase 2
0.5663 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5658 Remote Similarity NPD225 Approved
0.5658 Remote Similarity NPD227 Approved
0.5652 Remote Similarity NPD3704 Approved
0.5645 Remote Similarity NPD3728 Approved
0.5645 Remote Similarity NPD3730 Approved
0.5645 Remote Similarity NPD3729 Clinical (unspecified phase)
0.5641 Remote Similarity NPD4790 Discontinued
0.5641 Remote Similarity NPD857 Phase 3
0.561 Remote Similarity NPD3573 Approved
0.561 Remote Similarity NPD4793 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