Structure

Physi-Chem Properties

Molecular Weight:  279.23
Volume:  328.237
LogP:  2.692
LogD:  2.297
LogS:  -3.037
# Rotatable Bonds:  14
TPSA:  40.13
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.346
Synthetic Accessibility Score:  2.805
Fsp3:  0.722
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.904
MDCK Permeability:  4.570097371470183e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.033
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.096
Plasma Protein Binding (PPB):  98.30847930908203%
Volume Distribution (VD):  0.765
Pgp-substrate:  0.6111533641815186%

ADMET: Metabolism

CYP1A2-inhibitor:  0.32
CYP1A2-substrate:  0.539
CYP2C19-inhibitor:  0.442
CYP2C19-substrate:  0.204
CYP2C9-inhibitor:  0.53
CYP2C9-substrate:  0.988
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.258
CYP3A4-inhibitor:  0.181
CYP3A4-substrate:  0.042

ADMET: Excretion

Clearance (CL):  3.734
Half-life (T1/2):  0.816

ADMET: Toxicity

hERG Blockers:  0.065
Human Hepatotoxicity (H-HT):  0.343
Drug-inuced Liver Injury (DILI):  0.03
AMES Toxicity:  0.276
Rat Oral Acute Toxicity:  0.045
Maximum Recommended Daily Dose:  0.079
Skin Sensitization:  0.957
Carcinogencity:  0.421
Eye Corrosion:  0.878
Eye Irritation:  0.805
Respiratory Toxicity:  0.687

Download Data

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

  Natural Product: NPC224227

Natural Product ID:  NPC224227
Common Name*:   Sodium Linolate
IUPAC Name:   sodium;(9Z,12Z)-octadeca-9,12-dienoate
Synonyms:   Sodium Linolate
Standard InCHIKey:  WYPBVHPKMJYUEO-NBTZWHCOSA-M
Standard InCHI:  InChI=1S/C18H32O2.Na/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20;/h6-7,9-10H,2-5,8,11-17H2,1H3,(H,19,20);/q;+1/p-1/b7-6-,10-9-;
SMILES:  CCCCC/C=CC/C=CCCCCCCCC(=O)[O-].[Na+]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL571449
PubChem CID:   23676150
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000504] Lineolic acids and derivatives

*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 = 13600.0 nM PMID[558222]
NPT2 Others Unspecified Kd = 130000.0 nM PMID[558221]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Activity = 0.76 ml/cm PMID[558221]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Activity = 1.0 ml PMID[558221]

☑ 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 NPC224227 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 NPC262968
0.9388 High Similarity NPC309606
0.9388 High Similarity NPC139029
0.9388 High Similarity NPC1813
0.9388 High Similarity NPC36061
0.9388 High Similarity NPC294548
0.9388 High Similarity NPC39633
0.9388 High Similarity NPC139545
0.92 High Similarity NPC6095
0.92 High Similarity NPC261831
0.92 High Similarity NPC424
0.92 High Similarity NPC32467
0.92 High Similarity NPC85813
0.92 High Similarity NPC25417
0.92 High Similarity NPC154245
0.92 High Similarity NPC290563
0.92 High Similarity NPC88966
0.92 High Similarity NPC281972
0.92 High Similarity NPC87564
0.9184 High Similarity NPC281245
0.902 High Similarity NPC223677
0.902 High Similarity NPC10316
0.902 High Similarity NPC228473
0.902 High Similarity NPC128061
0.902 High Similarity NPC200845
0.902 High Similarity NPC28779
0.9 High Similarity NPC70387
0.9 High Similarity NPC71761
0.9 High Similarity NPC321062
0.8846 High Similarity NPC179764
0.8846 High Similarity NPC477201
0.8846 High Similarity NPC187777
0.8846 High Similarity NPC18951
0.88 High Similarity NPC92114
0.875 High Similarity NPC216130
0.8679 High Similarity NPC225929
0.8654 High Similarity NPC54766
0.8654 High Similarity NPC274290
0.8654 High Similarity NPC473863
0.8571 High Similarity NPC5413
0.8571 High Similarity NPC149821
0.8431 Intermediate Similarity NPC161366
0.84 Intermediate Similarity NPC59051
0.8367 Intermediate Similarity NPC180534
0.8367 Intermediate Similarity NPC207292
0.8364 Intermediate Similarity NPC106851
0.8364 Intermediate Similarity NPC274927
0.8214 Intermediate Similarity NPC235242
0.8214 Intermediate Similarity NPC174447
0.8214 Intermediate Similarity NPC229252
0.8214 Intermediate Similarity NPC122521
0.8214 Intermediate Similarity NPC251042
0.8214 Intermediate Similarity NPC243532
0.8214 Intermediate Similarity NPC143857
0.82 Intermediate Similarity NPC207815
0.8077 Intermediate Similarity NPC18357
0.807 Intermediate Similarity NPC201939
0.807 Intermediate Similarity NPC40082
0.8 Intermediate Similarity NPC91495
0.7959 Intermediate Similarity NPC117572
0.7931 Intermediate Similarity NPC54925
0.7885 Intermediate Similarity NPC470410
0.7885 Intermediate Similarity NPC28205
0.7885 Intermediate Similarity NPC284212
0.7885 Intermediate Similarity NPC470412
0.7857 Intermediate Similarity NPC267817
0.7857 Intermediate Similarity NPC34416
0.7843 Intermediate Similarity NPC163345
0.7797 Intermediate Similarity NPC470320
0.7797 Intermediate Similarity NPC328089
0.7797 Intermediate Similarity NPC68343
0.7778 Intermediate Similarity NPC87394
0.7759 Intermediate Similarity NPC125312
0.7759 Intermediate Similarity NPC174560
0.7667 Intermediate Similarity NPC255863
0.7667 Intermediate Similarity NPC326268
0.7667 Intermediate Similarity NPC318420
0.7667 Intermediate Similarity NPC136164
0.7667 Intermediate Similarity NPC245947
0.7636 Intermediate Similarity NPC474672
0.7636 Intermediate Similarity NPC477984
0.7636 Intermediate Similarity NPC52264
0.76 Intermediate Similarity NPC239754
0.7547 Intermediate Similarity NPC48162
0.75 Intermediate Similarity NPC325977
0.75 Intermediate Similarity NPC226592
0.7458 Intermediate Similarity NPC320305
0.7458 Intermediate Similarity NPC328776
0.7458 Intermediate Similarity NPC321838
0.7455 Intermediate Similarity NPC137538
0.7451 Intermediate Similarity NPC110234
0.7451 Intermediate Similarity NPC163751
0.7451 Intermediate Similarity NPC44363
0.7419 Intermediate Similarity NPC127091
0.7419 Intermediate Similarity NPC148192
0.7419 Intermediate Similarity NPC271921
0.7419 Intermediate Similarity NPC475443
0.7419 Intermediate Similarity NPC330426
0.7419 Intermediate Similarity NPC473829
0.7419 Intermediate Similarity NPC104537
0.7419 Intermediate Similarity NPC22101
0.7419 Intermediate Similarity NPC26500
0.7419 Intermediate Similarity NPC99619
0.7407 Intermediate Similarity NPC310746
0.7407 Intermediate Similarity NPC216407
0.7321 Intermediate Similarity NPC45626
0.7302 Intermediate Similarity NPC218477
0.7302 Intermediate Similarity NPC324981
0.7302 Intermediate Similarity NPC473559
0.7302 Intermediate Similarity NPC48218
0.7302 Intermediate Similarity NPC476614
0.7302 Intermediate Similarity NPC141481
0.7288 Intermediate Similarity NPC45097
0.7258 Intermediate Similarity NPC154728
0.7258 Intermediate Similarity NPC126899
0.7258 Intermediate Similarity NPC304665
0.7241 Intermediate Similarity NPC329819
0.7222 Intermediate Similarity NPC477458
0.7213 Intermediate Similarity NPC234767
0.72 Intermediate Similarity NPC270796
0.7188 Intermediate Similarity NPC317583
0.7188 Intermediate Similarity NPC473772
0.7188 Intermediate Similarity NPC143396
0.717 Intermediate Similarity NPC250919
0.7167 Intermediate Similarity NPC477829
0.7143 Intermediate Similarity NPC322461
0.7143 Intermediate Similarity NPC60120
0.7119 Intermediate Similarity NPC329550
0.7115 Intermediate Similarity NPC42304
0.7091 Intermediate Similarity NPC129458
0.7077 Intermediate Similarity NPC42526
0.7077 Intermediate Similarity NPC476660
0.7049 Intermediate Similarity NPC477707
0.7037 Intermediate Similarity NPC474391
0.7031 Intermediate Similarity NPC53302
0.7 Intermediate Similarity NPC328311
0.7 Intermediate Similarity NPC327112
0.6984 Remote Similarity NPC142423
0.6984 Remote Similarity NPC308294
0.6964 Remote Similarity NPC225066
0.6964 Remote Similarity NPC10081
0.6957 Remote Similarity NPC156630
0.6949 Remote Similarity NPC469373
0.6939 Remote Similarity NPC161097
0.6939 Remote Similarity NPC28598
0.6939 Remote Similarity NPC12156
0.6923 Remote Similarity NPC199557
0.6897 Remote Similarity NPC327388
0.6875 Remote Similarity NPC201622
0.6875 Remote Similarity NPC22903
0.6875 Remote Similarity NPC54980
0.6875 Remote Similarity NPC155880
0.6875 Remote Similarity NPC305660
0.6875 Remote Similarity NPC92863
0.6866 Remote Similarity NPC474705
0.6866 Remote Similarity NPC470237
0.6866 Remote Similarity NPC167145
0.6852 Remote Similarity NPC98284
0.6833 Remote Similarity NPC474267
0.6818 Remote Similarity NPC475310
0.68 Remote Similarity NPC216630
0.68 Remote Similarity NPC171736
0.68 Remote Similarity NPC307783
0.68 Remote Similarity NPC196924
0.68 Remote Similarity NPC149184
0.68 Remote Similarity NPC209970
0.6786 Remote Similarity NPC303765
0.6786 Remote Similarity NPC170167
0.678 Remote Similarity NPC211752
0.678 Remote Similarity NPC323498
0.678 Remote Similarity NPC323597
0.678 Remote Similarity NPC323436
0.6774 Remote Similarity NPC477830
0.6769 Remote Similarity NPC134385
0.6765 Remote Similarity NPC55527
0.6765 Remote Similarity NPC103958
0.6765 Remote Similarity NPC227396
0.6765 Remote Similarity NPC476046
0.6765 Remote Similarity NPC241854
0.6765 Remote Similarity NPC283908
0.6765 Remote Similarity NPC166797
0.6765 Remote Similarity NPC183503
0.6765 Remote Similarity NPC251970
0.6765 Remote Similarity NPC330016
0.6765 Remote Similarity NPC237591
0.6765 Remote Similarity NPC3753
0.6765 Remote Similarity NPC474321
0.6765 Remote Similarity NPC161923
0.6735 Remote Similarity NPC14227
0.6735 Remote Similarity NPC261080
0.6735 Remote Similarity NPC301585
0.6735 Remote Similarity NPC219536
0.6735 Remote Similarity NPC201844
0.6735 Remote Similarity NPC113928
0.6735 Remote Similarity NPC301696
0.6735 Remote Similarity NPC154186
0.6735 Remote Similarity NPC31551
0.6735 Remote Similarity NPC279026
0.6721 Remote Similarity NPC299730
0.6719 Remote Similarity NPC284447

  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 NPC224227 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
0.9787 High Similarity NPD28 Approved
0.9787 High Similarity NPD29 Approved
0.9388 High Similarity NPD3172 Approved
0.92 High Similarity NPD3194 Approved
0.92 High Similarity NPD3196 Approved
0.92 High Similarity NPD4266 Approved
0.92 High Similarity NPD3195 Phase 2
0.913 High Similarity NPD3174 Discontinued
0.8571 High Similarity NPD3173 Approved
0.8367 Intermediate Similarity NPD622 Approved
0.7959 Intermediate Similarity NPD4222 Approved
0.7797 Intermediate Similarity NPD3197 Phase 1
0.7647 Intermediate Similarity NPD5343 Approved
0.76 Intermediate Similarity NPD39 Approved
0.7234 Intermediate Similarity NPD3206 Approved
0.72 Intermediate Similarity NPD5326 Phase 3
0.7059 Intermediate Similarity NPD6096 Approved
0.7059 Intermediate Similarity NPD6097 Approved
0.7 Intermediate Similarity NPD4246 Clinical (unspecified phase)
0.68 Remote Similarity NPD2270 Approved
0.6735 Remote Similarity NPD9448 Phase 2
0.6735 Remote Similarity NPD633 Phase 3
0.6719 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6667 Remote Similarity NPD8039 Approved
0.6508 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6462 Remote Similarity NPD7331 Phase 2
0.6415 Remote Similarity NPD2699 Approved
0.6415 Remote Similarity NPD3199 Clinical (unspecified phase)
0.64 Remote Similarity NPD9655 Approved
0.6389 Remote Similarity NPD3732 Approved
0.6364 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6346 Remote Similarity NPD387 Clinical (unspecified phase)
0.6316 Remote Similarity NPD6927 Phase 3
0.625 Remote Similarity NPD4756 Discovery
0.6216 Remote Similarity NPD5368 Approved
0.6164 Remote Similarity NPD5784 Clinical (unspecified phase)
0.6133 Remote Similarity NPD5369 Approved
0.6129 Remote Similarity NPD6109 Phase 1
0.6078 Remote Similarity NPD5783 Phase 3
0.6053 Remote Similarity NPD4270 Approved
0.6053 Remote Similarity NPD6435 Approved
0.6053 Remote Similarity NPD4269 Approved
0.6 Remote Similarity NPD634 Phase 3
0.6 Remote Similarity NPD4252 Approved
0.5974 Remote Similarity NPD5362 Discontinued
0.5974 Remote Similarity NPD7154 Phase 3
0.5965 Remote Similarity NPD4220 Pre-registration
0.5946 Remote Similarity NPD4268 Approved
0.5946 Remote Similarity NPD4271 Approved
0.5844 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5823 Remote Similarity NPD5363 Approved
0.5821 Remote Similarity NPD7341 Phase 2
0.5821 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5789 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5789 Remote Similarity NPD4821 Approved
0.5789 Remote Similarity NPD6125 Clinical (unspecified phase)
0.5789 Remote Similarity NPD4822 Approved
0.5789 Remote Similarity NPD4820 Approved
0.5789 Remote Similarity NPD4819 Approved
0.575 Remote Similarity NPD5786 Approved
0.5735 Remote Similarity NPD3704 Approved
0.5733 Remote Similarity NPD225 Approved
0.5733 Remote Similarity NPD227 Approved
0.5714 Remote Similarity NPD857 Phase 3
0.5686 Remote Similarity NPD9449 Clinical (unspecified phase)
0.5679 Remote Similarity NPD3573 Approved
0.5667 Remote Similarity NPD3186 Phase 1
0.5645 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5606 Remote Similarity NPD4193 Approved
0.5606 Remote Similarity NPD4192 Approved
0.5606 Remote Similarity NPD4191 Approved
0.5606 Remote Similarity NPD4194 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