Structure

Physi-Chem Properties

Molecular Weight:  403.2
Volume:  420.226
LogP:  3.975
LogD:  2.72
LogS:  -3.765
# Rotatable Bonds:  15
TPSA:  46.17
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.367
Synthetic Accessibility Score:  4.255
Fsp3:  0.714
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:  -4.412
MDCK Permeability:  1.1034041563107166e-05
Pgp-inhibitor:  0.021
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.024
20% Bioavailability (F20%):  0.008
30% Bioavailability (F30%):  0.017

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.831
Plasma Protein Binding (PPB):  76.86746978759766%
Volume Distribution (VD):  0.715
Pgp-substrate:  4.029853343963623%

ADMET: Metabolism

CYP1A2-inhibitor:  0.466
CYP1A2-substrate:  0.761
CYP2C19-inhibitor:  0.907
CYP2C19-substrate:  0.302
CYP2C9-inhibitor:  0.878
CYP2C9-substrate:  0.847
CYP2D6-inhibitor:  0.337
CYP2D6-substrate:  0.693
CYP3A4-inhibitor:  0.95
CYP3A4-substrate:  0.365

ADMET: Excretion

Clearance (CL):  5.311
Half-life (T1/2):  0.878

ADMET: Toxicity

hERG Blockers:  0.048
Human Hepatotoxicity (H-HT):  0.924
Drug-inuced Liver Injury (DILI):  0.718
AMES Toxicity:  0.032
Rat Oral Acute Toxicity:  0.91
Maximum Recommended Daily Dose:  0.255
Skin Sensitization:  0.155
Carcinogencity:  0.49
Eye Corrosion:  0.003
Eye Irritation:  0.015
Respiratory Toxicity:  0.138

Download Data

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

  Natural Product: NPC469517

Natural Product ID:  NPC469517
Common Name*:   Grenadamide
IUPAC Name:   (5E)-N-[(E)-10-chloro-4,6-dimethyl-5-oxodec-9-en-2-yl]-5-(chloromethylidene)octanamide
Synonyms:   Grenadamide
Standard InCHIKey:  OEEXJHFQVSGEBK-KFPQZNHNSA-N
Standard InCHI:  InChI=1S/C21H35Cl2NO2/c1-5-9-19(15-23)11-8-12-20(25)24-18(4)14-17(3)21(26)16(2)10-6-7-13-22/h7,13,15-18H,5-6,8-12,14H2,1-4H3,(H,24,25)/b13-7+,19-15+
SMILES:  CCC/C(=CCl)/CCCC(=NC(CC(C(=O)C(CC/C=C/Cl)C)C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1081871
PubChem CID:   44479218
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000331] Fatty amides
          • [CHEMONTID:0001096] N-acyl amines

*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
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10514329]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10654420]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10691708]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. palauan n.a. PMID[10691729]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10843570]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10924172]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[10978206]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11076571]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11076573]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11076574]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11277744]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11389621]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11430000]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11473443]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[11922791]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[12762816]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Papua New Guinea n.a. PMID[12828459]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[14575437]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[1517734]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Papua New Guinea n.a. PMID[16643028]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[17125217]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[17441769]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[18444683]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Singapore n.a. PMID[19093843]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[19489598]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. eastern Caribbean n.a. PMID[19739598]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[19839606]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[20030365]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. panamanian n.a. PMID[20158242]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Floridian n.a. PMID[20166701]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[20936843]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21138309]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[2128518]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21341718]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21539315]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21806011]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[21999614]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[22035372]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[29792428]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[3924698]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Caribbean n.a. PMID[7623050]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. Caribbean n.a. PMID[8699186]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9584405]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9599278]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9599279]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria n.a. n.a. n.a. PMID[9784156]
NPO26389 Lyngbya majuscula Species Oscillatoriaceae Bacteria 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
NPT71 Cell Line HEK293 Homo sapiens IC50 >= 100000.0 nM PMID[555715]
NPT2779 Organism Spodoptera exigua Spodoptera exigua Activity = 50.0 % PMID[555715]

☑ 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 NPC469517 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
0.9863 High Similarity NPC469492
0.6731 Remote Similarity NPC46764
0.6711 Remote Similarity NPC210999
0.6471 Remote Similarity NPC474563
0.6413 Remote Similarity NPC477199
0.6386 Remote Similarity NPC474812
0.6337 Remote Similarity NPC233932
0.6289 Remote Similarity NPC314500
0.6226 Remote Similarity NPC140251
0.6226 Remote Similarity NPC307903
0.6224 Remote Similarity NPC472613
0.6196 Remote Similarity NPC39966
0.6174 Remote Similarity NPC16709
0.6173 Remote Similarity NPC316674
0.6146 Remote Similarity NPC316186
0.6132 Remote Similarity NPC475800
0.6129 Remote Similarity NPC471595
0.6106 Remote Similarity NPC323532
0.6105 Remote Similarity NPC322672
0.6095 Remote Similarity NPC259476
0.6042 Remote Similarity NPC473525
0.6042 Remote Similarity NPC472614
0.6022 Remote Similarity NPC224072
0.6019 Remote Similarity NPC474725
0.6 Remote Similarity NPC325550
0.6 Remote Similarity NPC477290
0.6 Remote Similarity NPC329003
0.6 Remote Similarity NPC319913
0.6 Remote Similarity NPC326524
0.5955 Remote Similarity NPC217095
0.5955 Remote Similarity NPC264417
0.5952 Remote Similarity NPC187315
0.593 Remote Similarity NPC291196
0.593 Remote Similarity NPC103712
0.5926 Remote Similarity NPC207820
0.5909 Remote Similarity NPC43219
0.5905 Remote Similarity NPC128501
0.5882 Remote Similarity NPC278895
0.5882 Remote Similarity NPC123141
0.5882 Remote Similarity NPC470110
0.5875 Remote Similarity NPC321030
0.5872 Remote Similarity NPC473578
0.5856 Remote Similarity NPC7797
0.5849 Remote Similarity NPC471317
0.5843 Remote Similarity NPC86064
0.5842 Remote Similarity NPC116930
0.5824 Remote Similarity NPC316242
0.5816 Remote Similarity NPC34754
0.5794 Remote Similarity NPC119329
0.5789 Remote Similarity NPC216335
0.578 Remote Similarity NPC168733
0.578 Remote Similarity NPC171734
0.578 Remote Similarity NPC475150
0.5769 Remote Similarity NPC234542
0.5766 Remote Similarity NPC12270
0.5765 Remote Similarity NPC470109
0.5765 Remote Similarity NPC197089
0.5763 Remote Similarity NPC280498
0.5761 Remote Similarity NPC478017
0.5761 Remote Similarity NPC474833
0.5761 Remote Similarity NPC315131
0.5761 Remote Similarity NPC315535
0.5758 Remote Similarity NPC39290
0.5758 Remote Similarity NPC159369
0.5752 Remote Similarity NPC471645
0.5747 Remote Similarity NPC469914
0.5741 Remote Similarity NPC472615
0.5741 Remote Similarity NPC271269
0.5741 Remote Similarity NPC154601
0.5732 Remote Similarity NPC40206
0.5732 Remote Similarity NPC6795
0.5728 Remote Similarity NPC476449
0.5726 Remote Similarity NPC78189
0.5714 Remote Similarity NPC324506
0.5714 Remote Similarity NPC469865
0.5714 Remote Similarity NPC473224
0.5714 Remote Similarity NPC204639
0.5702 Remote Similarity NPC471318
0.5701 Remote Similarity NPC476877
0.5701 Remote Similarity NPC202613
0.5699 Remote Similarity NPC471597
0.5698 Remote Similarity NPC195165
0.5691 Remote Similarity NPC96425
0.5688 Remote Similarity NPC251330
0.5684 Remote Similarity NPC474312
0.5684 Remote Similarity NPC473810
0.5682 Remote Similarity NPC477200
0.5679 Remote Similarity NPC325734
0.5676 Remote Similarity NPC92829
0.5673 Remote Similarity NPC4834
0.5667 Remote Similarity NPC288086
0.5667 Remote Similarity NPC469835
0.5663 Remote Similarity NPC124849
0.5663 Remote Similarity NPC21848
0.5663 Remote Similarity NPC174560
0.5663 Remote Similarity NPC125312
0.5652 Remote Similarity NPC188010
0.5648 Remote Similarity NPC472616
0.5647 Remote Similarity NPC470108
0.5632 Remote Similarity NPC476614
0.5614 Remote Similarity NPC50694
0.5614 Remote Similarity NPC24462
0.5614 Remote Similarity NPC476814
0.5614 Remote Similarity NPC476813
0.5607 Remote Similarity NPC469598
0.5607 Remote Similarity NPC152718
0.5607 Remote Similarity NPC226509
0.56 Remote Similarity NPC249312

  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 NPC469517 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
0.6224 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5818 Remote Similarity NPD6420 Discontinued
0.5766 Remote Similarity NPD1719 Phase 1
0.5765 Remote Similarity NPD7331 Phase 2
0.5761 Remote Similarity NPD7918 Clinical (unspecified phase)
0.5761 Remote Similarity NPD7917 Clinical (unspecified phase)
0.5745 Remote Similarity NPD857 Phase 3
0.5727 Remote Similarity NPD6413 Approved
0.5686 Remote Similarity NPD5769 Clinical (unspecified phase)
0.5663 Remote Similarity NPD835 Approved
0.5663 Remote Similarity NPD834 Approved
0.5625 Remote Similarity NPD3643 Approved
0.5625 Remote Similarity NPD3644 Approved
0.5625 Remote Similarity NPD3642 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