Structure

Physi-Chem Properties

Molecular Weight:  198.2
Volume:  239.558
LogP:  4.413
LogD:  4.177
LogS:  -4.106
# Rotatable Bonds:  10
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.472
Synthetic Accessibility Score:  1.814
Fsp3:  0.923
Lipinski Rule-of-5:  Accepted
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:  -4.566
MDCK Permeability:  1.354070809611585e-05
Pgp-inhibitor:  0.456
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.995
30% Bioavailability (F30%):  0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.987
Plasma Protein Binding (PPB):  94.64517211914062%
Volume Distribution (VD):  1.109
Pgp-substrate:  3.0534985065460205%

ADMET: Metabolism

CYP1A2-inhibitor:  0.759
CYP1A2-substrate:  0.562
CYP2C19-inhibitor:  0.444
CYP2C19-substrate:  0.174
CYP2C9-inhibitor:  0.348
CYP2C9-substrate:  0.937
CYP2D6-inhibitor:  0.019
CYP2D6-substrate:  0.394
CYP3A4-inhibitor:  0.128
CYP3A4-substrate:  0.084

ADMET: Excretion

Clearance (CL):  7.05
Half-life (T1/2):  0.777

ADMET: Toxicity

hERG Blockers:  0.077
Human Hepatotoxicity (H-HT):  0.045
Drug-inuced Liver Injury (DILI):  0.073
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.06
Maximum Recommended Daily Dose:  0.022
Skin Sensitization:  0.516
Carcinogencity:  0.054
Eye Corrosion:  0.914
Eye Irritation:  0.975
Respiratory Toxicity:  0.829

Download Data

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

  Natural Product: NPC79887

Natural Product ID:  NPC79887
Common Name*:   4-Tridecanone
IUPAC Name:   tridecan-4-one
Synonyms:   4-Tridecanone
Standard InCHIKey:  JWSRUPAFLPWLNO-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C13H26O/c1-3-5-6-7-8-9-10-12-13(14)11-4-2/h3-12H2,1-2H3
SMILES:  CCCCCCCCCC(=O)CCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1922860
PubChem CID:   98673
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones

*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
NPO1436 Houttuynia cordata Species Saururaceae Eukaryota n.a. n.a. n.a. PMID[29099182]
NPO1436 Houttuynia cordata Species Saururaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1436 Houttuynia cordata Species Saururaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1436 Houttuynia cordata Species Saururaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1436 Houttuynia cordata Species Saururaceae 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
NPT3943 Individual Protein CAI-1 autoinducer sensor kinase/phosphatase CqsS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) EC50 > 50000.0 nM PMID[555921]
NPT3943 Individual Protein CAI-1 autoinducer sensor kinase/phosphatase CqsS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) Ratio EC50 > 200.0 n.a. PMID[555921]

☑ 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 NPC79887 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 NPC221192
1.0 High Similarity NPC29561
1.0 High Similarity NPC196434
1.0 High Similarity NPC4962
1.0 High Similarity NPC222997
1.0 High Similarity NPC42403
1.0 High Similarity NPC153439
0.9643 High Similarity NPC168982
0.963 High Similarity NPC295442
0.963 High Similarity NPC38859
0.963 High Similarity NPC198118
0.931 High Similarity NPC225318
0.931 High Similarity NPC149101
0.931 High Similarity NPC268596
0.931 High Similarity NPC16578
0.931 High Similarity NPC76608
0.8621 High Similarity NPC158107
0.8519 High Similarity NPC66624
0.8214 Intermediate Similarity NPC79591
0.8182 Intermediate Similarity NPC301919
0.8065 Intermediate Similarity NPC179831
0.8065 Intermediate Similarity NPC254713
0.8065 Intermediate Similarity NPC49151
0.8065 Intermediate Similarity NPC261991
0.8065 Intermediate Similarity NPC262505
0.7714 Intermediate Similarity NPC223315
0.7576 Intermediate Similarity NPC49615
0.75 Intermediate Similarity NPC141634
0.75 Intermediate Similarity NPC30338
0.7407 Intermediate Similarity NPC32603
0.7297 Intermediate Similarity NPC45270
0.7297 Intermediate Similarity NPC59570
0.7297 Intermediate Similarity NPC135077
0.7297 Intermediate Similarity NPC215118
0.7241 Intermediate Similarity NPC129976
0.7188 Intermediate Similarity NPC321646
0.7143 Intermediate Similarity NPC33928
0.7097 Intermediate Similarity NPC32279
0.7037 Intermediate Similarity NPC141986
0.6944 Remote Similarity NPC69245
0.6923 Remote Similarity NPC18397
0.6857 Remote Similarity NPC156630
0.6786 Remote Similarity NPC222945
0.6774 Remote Similarity NPC100997
0.6757 Remote Similarity NPC54980
0.6757 Remote Similarity NPC305660
0.6757 Remote Similarity NPC201622
0.6757 Remote Similarity NPC22903
0.675 Remote Similarity NPC74845
0.675 Remote Similarity NPC76051
0.6667 Remote Similarity NPC147212
0.6585 Remote Similarity NPC469781
0.6579 Remote Similarity NPC201844
0.6579 Remote Similarity NPC219536
0.6579 Remote Similarity NPC301696
0.6579 Remote Similarity NPC261080
0.6579 Remote Similarity NPC301585
0.6579 Remote Similarity NPC279026
0.6579 Remote Similarity NPC113928
0.6579 Remote Similarity NPC154186
0.6579 Remote Similarity NPC31551
0.6579 Remote Similarity NPC14227
0.6552 Remote Similarity NPC185768
0.6552 Remote Similarity NPC254524
0.65 Remote Similarity NPC473674
0.6486 Remote Similarity NPC220061
0.6452 Remote Similarity NPC59581
0.641 Remote Similarity NPC28598
0.641 Remote Similarity NPC40597
0.641 Remote Similarity NPC161097
0.641 Remote Similarity NPC256163
0.641 Remote Similarity NPC149299
0.641 Remote Similarity NPC250028
0.641 Remote Similarity NPC12156
0.6389 Remote Similarity NPC218357
0.6341 Remote Similarity NPC317128
0.6341 Remote Similarity NPC171783
0.6296 Remote Similarity NPC211453
0.6279 Remote Similarity NPC285814
0.6279 Remote Similarity NPC98246
0.6279 Remote Similarity NPC173996
0.6279 Remote Similarity NPC83187
0.6279 Remote Similarity NPC131981
0.6279 Remote Similarity NPC40249
0.625 Remote Similarity NPC209970
0.625 Remote Similarity NPC141914
0.625 Remote Similarity NPC149184
0.625 Remote Similarity NPC216630
0.625 Remote Similarity NPC196924
0.625 Remote Similarity NPC171736
0.625 Remote Similarity NPC53541
0.625 Remote Similarity NPC307783
0.619 Remote Similarity NPC47363
0.619 Remote Similarity NPC287231
0.6154 Remote Similarity NPC80234
0.6154 Remote Similarity NPC223249
0.6154 Remote Similarity NPC294085
0.6154 Remote Similarity NPC118968
0.6154 Remote Similarity NPC183424
0.6154 Remote Similarity NPC214610
0.6136 Remote Similarity NPC294440
0.6129 Remote Similarity NPC307594
0.6129 Remote Similarity NPC227197
0.6111 Remote Similarity NPC248190
0.6098 Remote Similarity NPC203531
0.6098 Remote Similarity NPC67462
0.6098 Remote Similarity NPC236579
0.6047 Remote Similarity NPC52700
0.6047 Remote Similarity NPC145045
0.6047 Remote Similarity NPC105329
0.6047 Remote Similarity NPC63182
0.6 Remote Similarity NPC165533
0.6 Remote Similarity NPC48930
0.6 Remote Similarity NPC145311
0.6 Remote Similarity NPC247786
0.6 Remote Similarity NPC258672
0.6 Remote Similarity NPC293343
0.5952 Remote Similarity NPC19305
0.5952 Remote Similarity NPC255837
0.5946 Remote Similarity NPC121215
0.5909 Remote Similarity NPC326957
0.5909 Remote Similarity NPC328497
0.5909 Remote Similarity NPC324004
0.5897 Remote Similarity NPC92863
0.5897 Remote Similarity NPC155880
0.5897 Remote Similarity NPC268826
0.587 Remote Similarity NPC474391
0.587 Remote Similarity NPC116906
0.5854 Remote Similarity NPC163746
0.5854 Remote Similarity NPC103286
0.5854 Remote Similarity NPC474361
0.5814 Remote Similarity NPC8219
0.5814 Remote Similarity NPC55023
0.5814 Remote Similarity NPC273545
0.5806 Remote Similarity NPC164646
0.5806 Remote Similarity NPC91093
0.5789 Remote Similarity NPC155263
0.5789 Remote Similarity NPC80396
0.5789 Remote Similarity NPC154642
0.5778 Remote Similarity NPC106872
0.5778 Remote Similarity NPC20017
0.5778 Remote Similarity NPC13105
0.5778 Remote Similarity NPC131770
0.5778 Remote Similarity NPC200618
0.5745 Remote Similarity NPC274182
0.5745 Remote Similarity NPC236623
0.5745 Remote Similarity NPC477458
0.5714 Remote Similarity NPC289686
0.5714 Remote Similarity NPC71317
0.5714 Remote Similarity NPC129972
0.5714 Remote Similarity NPC301528
0.5714 Remote Similarity NPC171188
0.5682 Remote Similarity NPC12438
0.5682 Remote Similarity NPC30195
0.5682 Remote Similarity NPC239754
0.5682 Remote Similarity NPC314679
0.5676 Remote Similarity NPC57499
0.5667 Remote Similarity NPC83723
0.5652 Remote Similarity NPC304162
0.5641 Remote Similarity NPC109026
0.5625 Remote Similarity NPC471607

  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 NPC79887 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
0.6757 Remote Similarity NPD3206 Approved
0.6579 Remote Similarity NPD633 Phase 3
0.6579 Remote Similarity NPD9448 Phase 2
0.6279 Remote Similarity NPD343 Approved
0.6279 Remote Similarity NPD345 Approved
0.6279 Remote Similarity NPD344 Approved
0.625 Remote Similarity NPD2270 Approved
0.619 Remote Similarity NPD2699 Approved
0.6154 Remote Similarity NPD9655 Approved
0.6098 Remote Similarity NPD387 Clinical (unspecified phase)
0.5814 Remote Similarity NPD3199 Clinical (unspecified phase)
0.5682 Remote Similarity NPD634 Phase 3
0.5641 Remote Similarity NPD9449 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