Structure

Physi-Chem Properties

Molecular Weight:  327.24
Volume:  358.132
LogP:  5.961
LogD:  3.795
LogS:  -4.716
# Rotatable Bonds:  16
TPSA:  80.44
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.223
Synthetic Accessibility Score:  2.474
Fsp3:  0.833
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.971
MDCK Permeability:  4.8969446652336046e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.852

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.017
Plasma Protein Binding (PPB):  98.93914031982422%
Volume Distribution (VD):  0.686
Pgp-substrate:  0.6699867844581604%

ADMET: Metabolism

CYP1A2-inhibitor:  0.287
CYP1A2-substrate:  0.308
CYP2C19-inhibitor:  0.482
CYP2C19-substrate:  0.153
CYP2C9-inhibitor:  0.503
CYP2C9-substrate:  0.992
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.152
CYP3A4-inhibitor:  0.068
CYP3A4-substrate:  0.021

ADMET: Excretion

Clearance (CL):  2.329
Half-life (T1/2):  0.76

ADMET: Toxicity

hERG Blockers:  0.026
Human Hepatotoxicity (H-HT):  0.445
Drug-inuced Liver Injury (DILI):  0.043
AMES Toxicity:  0.183
Rat Oral Acute Toxicity:  0.018
Maximum Recommended Daily Dose:  0.059
Skin Sensitization:  0.941
Carcinogencity:  0.251
Eye Corrosion:  0.118
Eye Irritation:  0.825
Respiratory Toxicity:  0.907

Download Data

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

  Natural Product: NPC320669

Natural Product ID:  NPC320669
Common Name*:   (E)-10-Nitrooctadec-9-Enoic Acid
IUPAC Name:   (E)-10-nitrooctadec-9-enoic acid
Synonyms:  
Standard InCHIKey:  WRADPCFZZWXOTI-BMRADRMJSA-N
Standard InCHI:  InChI=1S/C18H33NO4/c1-2-3-4-5-8-11-14-17(19(22)23)15-12-9-6-7-10-13-16-18(20)21/h15H,2-14,16H2,1H3,(H,20,21)/b17-15+
SMILES:  CCCCCCCCC(=CCCCCCCCC(=O)O)[N+](=O)[O-]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL561371
PubChem CID:   24836820
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

☑ 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
NPT99 Individual Protein Peroxisome proliferator-activated receptor gamma Homo sapiens IC50 = 1610.0 nM PMID[496787]
NPT866 Individual Protein Peroxisome proliferator-activated receptor alpha Homo sapiens IC50 > 15000.0 nM PMID[496787]

☑ 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 NPC320669 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 NPC318814
0.7313 Intermediate Similarity NPC6095
0.7313 Intermediate Similarity NPC281972
0.7313 Intermediate Similarity NPC88966
0.7313 Intermediate Similarity NPC85813
0.7313 Intermediate Similarity NPC154245
0.7313 Intermediate Similarity NPC424
0.7313 Intermediate Similarity NPC87564
0.7313 Intermediate Similarity NPC32467
0.7313 Intermediate Similarity NPC25417
0.7313 Intermediate Similarity NPC290563
0.7313 Intermediate Similarity NPC261831
0.7164 Intermediate Similarity NPC70387
0.7164 Intermediate Similarity NPC321062
0.7164 Intermediate Similarity NPC1813
0.7164 Intermediate Similarity NPC139029
0.7164 Intermediate Similarity NPC294548
0.7164 Intermediate Similarity NPC36061
0.7101 Intermediate Similarity NPC18951
0.7101 Intermediate Similarity NPC477201
0.7015 Intermediate Similarity NPC92114
0.7015 Intermediate Similarity NPC281245
0.6866 Remote Similarity NPC262968
0.6857 Remote Similarity NPC179764
0.6857 Remote Similarity NPC187777
0.6806 Remote Similarity NPC106851
0.6806 Remote Similarity NPC274927
0.6761 Remote Similarity NPC225929
0.6716 Remote Similarity NPC59051
0.6716 Remote Similarity NPC224227
0.6714 Remote Similarity NPC274290
0.6714 Remote Similarity NPC473863
0.6714 Remote Similarity NPC54766
0.6712 Remote Similarity NPC243532
0.6667 Remote Similarity NPC309606
0.6667 Remote Similarity NPC139545
0.6667 Remote Similarity NPC39633
0.6622 Remote Similarity NPC201939
0.6622 Remote Similarity NPC40082
0.6579 Remote Similarity NPC326268
0.6579 Remote Similarity NPC318420
0.6571 Remote Similarity NPC87394
0.6567 Remote Similarity NPC5413
0.6567 Remote Similarity NPC149821
0.6486 Remote Similarity NPC174447
0.6486 Remote Similarity NPC235242
0.6486 Remote Similarity NPC251042
0.6486 Remote Similarity NPC122521
0.6479 Remote Similarity NPC128061
0.6479 Remote Similarity NPC10316
0.6479 Remote Similarity NPC200845
0.6479 Remote Similarity NPC28779
0.6479 Remote Similarity NPC223677
0.6479 Remote Similarity NPC228473
0.6447 Remote Similarity NPC68343
0.6447 Remote Similarity NPC328089
0.6438 Remote Similarity NPC34416
0.6418 Remote Similarity NPC180534
0.6418 Remote Similarity NPC207292
0.6418 Remote Similarity NPC91495
0.641 Remote Similarity NPC127091
0.641 Remote Similarity NPC22101
0.641 Remote Similarity NPC26500
0.641 Remote Similarity NPC99619
0.641 Remote Similarity NPC148192
0.641 Remote Similarity NPC271921
0.641 Remote Similarity NPC330426
0.641 Remote Similarity NPC104537
0.64 Remote Similarity NPC321838
0.64 Remote Similarity NPC125312
0.64 Remote Similarity NPC174560
0.6377 Remote Similarity NPC470410
0.6377 Remote Similarity NPC470412
0.6364 Remote Similarity NPC245947
0.6364 Remote Similarity NPC136164
0.6364 Remote Similarity NPC255863
0.6329 Remote Similarity NPC473559
0.6329 Remote Similarity NPC141481
0.6329 Remote Similarity NPC48218
0.6329 Remote Similarity NPC324981
0.6286 Remote Similarity NPC18357
0.6234 Remote Similarity NPC234767
0.6234 Remote Similarity NPC470320
0.6216 Remote Similarity NPC267817
0.6203 Remote Similarity NPC473829
0.6203 Remote Similarity NPC475443
0.6197 Remote Similarity NPC71761
0.6184 Remote Similarity NPC328776
0.6184 Remote Similarity NPC320305
0.6173 Remote Similarity NPC476660
0.6173 Remote Similarity NPC42526
0.6154 Remote Similarity NPC472614
0.6143 Remote Similarity NPC284212
0.6143 Remote Similarity NPC28205
0.6119 Remote Similarity NPC117572
0.6104 Remote Similarity NPC316674
0.6104 Remote Similarity NPC54925
0.6053 Remote Similarity NPC229252
0.6053 Remote Similarity NPC143857
0.6053 Remote Similarity NPC328311
0.6049 Remote Similarity NPC317583
0.6049 Remote Similarity NPC473772
0.6049 Remote Similarity NPC143396
0.6044 Remote Similarity NPC258824
0.6027 Remote Similarity NPC52264
0.6026 Remote Similarity NPC226592
0.5952 Remote Similarity NPC474321
0.5952 Remote Similarity NPC227396
0.5946 Remote Similarity NPC325977
0.5942 Remote Similarity NPC216130
0.5926 Remote Similarity NPC476614
0.5915 Remote Similarity NPC48162
0.5904 Remote Similarity NPC160817
0.5897 Remote Similarity NPC477707
0.589 Remote Similarity NPC137538
0.5875 Remote Similarity NPC142423
0.5875 Remote Similarity NPC308294
0.5875 Remote Similarity NPC60424
0.5875 Remote Similarity NPC314221
0.5867 Remote Similarity NPC323436
0.5851 Remote Similarity NPC39290
0.5851 Remote Similarity NPC159369
0.5844 Remote Similarity NPC327112
0.5833 Remote Similarity NPC161366
0.5833 Remote Similarity NPC325627
0.5833 Remote Similarity NPC472613
0.5823 Remote Similarity NPC7029
0.5821 Remote Similarity NPC270796
0.5814 Remote Similarity NPC469514
0.5814 Remote Similarity NPC279537
0.5811 Remote Similarity NPC45626
0.5802 Remote Similarity NPC60120
0.5789 Remote Similarity NPC477288
0.5789 Remote Similarity NPC474964
0.5789 Remote Similarity NPC236322
0.5789 Remote Similarity NPC329819
0.5789 Remote Similarity NPC47230
0.5789 Remote Similarity NPC17143
0.5783 Remote Similarity NPC67183
0.5769 Remote Similarity NPC477829
0.5758 Remote Similarity NPC196924
0.5758 Remote Similarity NPC149184
0.5758 Remote Similarity NPC216630
0.5758 Remote Similarity NPC209970
0.5758 Remote Similarity NPC307783
0.5758 Remote Similarity NPC171736
0.575 Remote Similarity NPC476654
0.575 Remote Similarity NPC320642
0.575 Remote Similarity NPC476655
0.575 Remote Similarity NPC476657
0.5747 Remote Similarity NPC120776
0.5747 Remote Similarity NPC281296
0.5747 Remote Similarity NPC240170
0.5732 Remote Similarity NPC53302
0.5729 Remote Similarity NPC476064
0.5728 Remote Similarity NPC472616
0.5714 Remote Similarity NPC329249
0.5714 Remote Similarity NPC178758
0.5714 Remote Similarity NPC329550
0.5714 Remote Similarity NPC196102
0.5698 Remote Similarity NPC199445
0.5698 Remote Similarity NPC476844
0.5696 Remote Similarity NPC477830
0.5696 Remote Similarity NPC143168
0.5696 Remote Similarity NPC53109
0.5694 Remote Similarity NPC477458
0.5682 Remote Similarity NPC321514
0.5682 Remote Similarity NPC192006
0.5682 Remote Similarity NPC110094
0.5682 Remote Similarity NPC121200
0.5682 Remote Similarity NPC280654
0.5682 Remote Similarity NPC474833
0.5682 Remote Similarity NPC260385
0.5679 Remote Similarity NPC476659
0.5679 Remote Similarity NPC476656
0.5676 Remote Similarity NPC322461
0.5673 Remote Similarity NPC472615
0.5672 Remote Similarity NPC67462
0.5663 Remote Similarity NPC470436
0.5663 Remote Similarity NPC67608
0.5658 Remote Similarity NPC323498
0.5658 Remote Similarity NPC323597
0.5658 Remote Similarity NPC211752
0.5652 Remote Similarity NPC477289
0.5647 Remote Similarity NPC326024
0.5641 Remote Similarity NPC321919
0.5641 Remote Similarity NPC45097
0.5641 Remote Similarity NPC81896
0.5634 Remote Similarity NPC207815
0.5632 Remote Similarity NPC180886
0.5618 Remote Similarity NPC196827
0.5618 Remote Similarity NPC327674
0.5618 Remote Similarity NPC199595
0.5618 Remote Similarity NPC469747
0.5618 Remote Similarity NPC263574
0.5618 Remote Similarity NPC308545
0.5618 Remote Similarity NPC274996
0.5618 Remote Similarity NPC82488
0.5616 Remote Similarity NPC129458
0.5616 Remote Similarity NPC188341

  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 NPC320669 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
0.7313 Intermediate Similarity NPD3194 Approved
0.7313 Intermediate Similarity NPD3195 Phase 2
0.7313 Intermediate Similarity NPD3196 Approved
0.7313 Intermediate Similarity NPD4266 Approved
0.7164 Intermediate Similarity NPD3172 Approved
0.6866 Remote Similarity NPD29 Approved
0.6866 Remote Similarity NPD28 Approved
0.6627 Remote Similarity NPD3732 Approved
0.6567 Remote Similarity NPD3173 Approved
0.6447 Remote Similarity NPD3197 Phase 1
0.6418 Remote Similarity NPD622 Approved
0.6119 Remote Similarity NPD39 Approved
0.6119 Remote Similarity NPD3174 Discontinued
0.6119 Remote Similarity NPD4222 Approved
0.5844 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5843 Remote Similarity NPD857 Phase 3
0.5821 Remote Similarity NPD5326 Phase 3
0.5758 Remote Similarity NPD2270 Approved
0.5696 Remote Similarity NPD2664 Clinical (unspecified phase)
0.5679 Remote Similarity NPD7331 Phase 2
0.561 Remote Similarity NPD4247 Clinical (unspecified phase)
0.561 Remote Similarity NPD3709 Clinical (unspecified phase)

  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