Structure

Physi-Chem Properties

Molecular Weight:  186.16
Volume:  213.756
LogP:  2.262
LogD:  2.41
LogS:  -1.923
# Rotatable Bonds:  7
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.571
Synthetic Accessibility Score:  3.28
Fsp3:  0.909
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.39
MDCK Permeability:  1.9366205378901213e-05
Pgp-inhibitor:  0.009
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.558
30% Bioavailability (F30%):  0.293

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.986
Plasma Protein Binding (PPB):  34.55339813232422%
Volume Distribution (VD):  1.378
Pgp-substrate:  63.83130645751953%

ADMET: Metabolism

CYP1A2-inhibitor:  0.071
CYP1A2-substrate:  0.765
CYP2C19-inhibitor:  0.079
CYP2C19-substrate:  0.84
CYP2C9-inhibitor:  0.03
CYP2C9-substrate:  0.585
CYP2D6-inhibitor:  0.028
CYP2D6-substrate:  0.551
CYP3A4-inhibitor:  0.027
CYP3A4-substrate:  0.223

ADMET: Excretion

Clearance (CL):  7.642
Half-life (T1/2):  0.574

ADMET: Toxicity

hERG Blockers:  0.026
Human Hepatotoxicity (H-HT):  0.03
Drug-inuced Liver Injury (DILI):  0.036
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.01
Maximum Recommended Daily Dose:  0.017
Skin Sensitization:  0.951
Carcinogencity:  0.076
Eye Corrosion:  0.978
Eye Irritation:  0.973
Respiratory Toxicity:  0.189

Download Data

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

  Natural Product: NPC13105

Natural Product ID:  NPC13105
Common Name*:   7-Methoxy-3,7-Dimethyloctanal
IUPAC Name:   7-methoxy-3,7-dimethyloctanal
Synonyms:  
Standard InCHIKey:  IDWULKZGRNHZNR-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H22O2/c1-10(7-9-12)6-5-8-11(2,3)13-4/h9-10H,5-8H2,1-4H3
SMILES:  CC(CCCC(C)(C)OC)CC=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3189093
PubChem CID:   19223
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000124] Aldehydes
            • [CHEMONTID:0002229] Medium-chain aldehydes

*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
NPT2 Others Unspecified Potency n.a. 96.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 54941 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68589.6 nM PubChem BioAssay data set

☑ 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 NPC13105 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
0.7843 Intermediate Similarity NPC314084
0.7727 Intermediate Similarity NPC69245
0.7647 Intermediate Similarity NPC305182
0.7273 Intermediate Similarity NPC218357
0.7241 Intermediate Similarity NPC472021
0.72 Intermediate Similarity NPC314679
0.7119 Intermediate Similarity NPC253204
0.7091 Intermediate Similarity NPC319589
0.7069 Intermediate Similarity NPC472019
0.7069 Intermediate Similarity NPC472020
0.7069 Intermediate Similarity NPC226602
0.7059 Intermediate Similarity NPC249754
0.7 Intermediate Similarity NPC55023
0.6923 Remote Similarity NPC477878
0.6923 Remote Similarity NPC324793
0.6875 Remote Similarity NPC250028
0.6875 Remote Similarity NPC149299
0.6875 Remote Similarity NPC40597
0.6875 Remote Similarity NPC256163
0.6863 Remote Similarity NPC308301
0.6863 Remote Similarity NPC282440
0.6809 Remote Similarity NPC305660
0.6809 Remote Similarity NPC201622
0.6809 Remote Similarity NPC22903
0.6809 Remote Similarity NPC54980
0.6809 Remote Similarity NPC223315
0.68 Remote Similarity NPC317128
0.678 Remote Similarity NPC475821
0.6774 Remote Similarity NPC306805
0.6774 Remote Similarity NPC476330
0.6774 Remote Similarity NPC215987
0.6739 Remote Similarity NPC301919
0.6735 Remote Similarity NPC53541
0.6731 Remote Similarity NPC21844
0.6721 Remote Similarity NPC235788
0.6721 Remote Similarity NPC474552
0.6719 Remote Similarity NPC478228
0.6667 Remote Similarity NPC223249
0.6667 Remote Similarity NPC287231
0.6667 Remote Similarity NPC80234
0.6667 Remote Similarity NPC141634
0.6667 Remote Similarity NPC219536
0.6667 Remote Similarity NPC31551
0.6667 Remote Similarity NPC47363
0.6667 Remote Similarity NPC478126
0.66 Remote Similarity NPC236579
0.66 Remote Similarity NPC203531
0.66 Remote Similarity NPC18397
0.6591 Remote Similarity NPC261991
0.6591 Remote Similarity NPC262505
0.6591 Remote Similarity NPC254713
0.6591 Remote Similarity NPC49151
0.6591 Remote Similarity NPC179831
0.6562 Remote Similarity NPC286842
0.6557 Remote Similarity NPC469922
0.6557 Remote Similarity NPC306750
0.6557 Remote Similarity NPC469923
0.6545 Remote Similarity NPC291724
0.6545 Remote Similarity NPC274261
0.6538 Remote Similarity NPC52700
0.6538 Remote Similarity NPC105329
0.6538 Remote Similarity NPC63182
0.6538 Remote Similarity NPC145045
0.6531 Remote Similarity NPC28598
0.6531 Remote Similarity NPC59570
0.6531 Remote Similarity NPC45270
0.6531 Remote Similarity NPC161097
0.6531 Remote Similarity NPC135077
0.6531 Remote Similarity NPC165533
0.6531 Remote Similarity NPC215118
0.6508 Remote Similarity NPC157518
0.65 Remote Similarity NPC469924
0.65 Remote Similarity NPC470363
0.6471 Remote Similarity NPC76051
0.6458 Remote Similarity NPC316546
0.6415 Remote Similarity NPC326957
0.6406 Remote Similarity NPC473899
0.64 Remote Similarity NPC325452
0.64 Remote Similarity NPC248763
0.6393 Remote Similarity NPC40206
0.6383 Remote Similarity NPC328441
0.6364 Remote Similarity NPC295788
0.6364 Remote Similarity NPC261398
0.6364 Remote Similarity NPC98711
0.6349 Remote Similarity NPC314103
0.6346 Remote Similarity NPC469781
0.6346 Remote Similarity NPC273545
0.6327 Remote Similarity NPC81263
0.6316 Remote Similarity NPC72722
0.6308 Remote Similarity NPC41542
0.6304 Remote Similarity NPC49615
0.6296 Remote Similarity NPC106872
0.6269 Remote Similarity NPC476731
0.625 Remote Similarity NPC469926
0.625 Remote Similarity NPC14608
0.625 Remote Similarity NPC177022
0.6226 Remote Similarity NPC30195
0.6226 Remote Similarity NPC12438
0.62 Remote Similarity NPC12156
0.6197 Remote Similarity NPC108014
0.6176 Remote Similarity NPC478227
0.617 Remote Similarity NPC156630
0.6154 Remote Similarity NPC302939
0.6154 Remote Similarity NPC287331
0.6154 Remote Similarity NPC315525
0.6154 Remote Similarity NPC84562
0.6154 Remote Similarity NPC135043
0.6143 Remote Similarity NPC24014
0.6143 Remote Similarity NPC27349
0.6129 Remote Similarity NPC469921
0.6119 Remote Similarity NPC178541
0.6119 Remote Similarity NPC477448
0.6119 Remote Similarity NPC5714
0.6119 Remote Similarity NPC477449
0.6119 Remote Similarity NPC64466
0.6111 Remote Similarity NPC328497
0.6111 Remote Similarity NPC207186
0.6111 Remote Similarity NPC324004
0.6094 Remote Similarity NPC128608
0.6087 Remote Similarity NPC107783
0.6087 Remote Similarity NPC92909
0.6087 Remote Similarity NPC109510
0.6087 Remote Similarity NPC474123
0.6071 Remote Similarity NPC55678
0.6071 Remote Similarity NPC142103
0.6061 Remote Similarity NPC328304
0.6061 Remote Similarity NPC472984
0.6061 Remote Similarity NPC469868
0.6061 Remote Similarity NPC469925
0.6061 Remote Similarity NPC329466
0.6056 Remote Similarity NPC215481
0.6042 Remote Similarity NPC80641
0.6042 Remote Similarity NPC154642
0.6042 Remote Similarity NPC80396
0.6029 Remote Similarity NPC280256
0.6029 Remote Similarity NPC475310
0.6 Remote Similarity NPC301585
0.6 Remote Similarity NPC167049
0.6 Remote Similarity NPC19311
0.6 Remote Similarity NPC474304
0.6 Remote Similarity NPC14227
0.6 Remote Similarity NPC261080
0.6 Remote Similarity NPC199316
0.6 Remote Similarity NPC221022
0.6 Remote Similarity NPC469691
0.6 Remote Similarity NPC321646
0.6 Remote Similarity NPC61473
0.6 Remote Similarity NPC102313
0.6 Remote Similarity NPC474329
0.6 Remote Similarity NPC113928
0.6 Remote Similarity NPC154186
0.6 Remote Similarity NPC200618
0.6 Remote Similarity NPC131770
0.6 Remote Similarity NPC330016
0.6 Remote Similarity NPC279026
0.6 Remote Similarity NPC230047
0.6 Remote Similarity NPC301696
0.6 Remote Similarity NPC3531
0.6 Remote Similarity NPC215030
0.6 Remote Similarity NPC201844
0.6 Remote Similarity NPC55508
0.6 Remote Similarity NPC168982
0.597 Remote Similarity NPC180777
0.597 Remote Similarity NPC319007
0.597 Remote Similarity NPC474954
0.597 Remote Similarity NPC82315
0.597 Remote Similarity NPC2568
0.597 Remote Similarity NPC103647
0.597 Remote Similarity NPC260319
0.5965 Remote Similarity NPC474331
0.5965 Remote Similarity NPC287811
0.5962 Remote Similarity NPC474126
0.5962 Remote Similarity NPC82843
0.5962 Remote Similarity NPC176500
0.5962 Remote Similarity NPC474125
0.5942 Remote Similarity NPC40327
0.5942 Remote Similarity NPC72343
0.5942 Remote Similarity NPC470243
0.5942 Remote Similarity NPC96322
0.5926 Remote Similarity NPC108441
0.5926 Remote Similarity NPC77550
0.5915 Remote Similarity NPC475861
0.5915 Remote Similarity NPC469678
0.5915 Remote Similarity NPC469669
0.5915 Remote Similarity NPC474419
0.5915 Remote Similarity NPC475771
0.5909 Remote Similarity NPC103734
0.5909 Remote Similarity NPC32279
0.5909 Remote Similarity NPC287782
0.5893 Remote Similarity NPC304162
0.5893 Remote Similarity NPC26253
0.589 Remote Similarity NPC80088
0.589 Remote Similarity NPC253561
0.5882 Remote Similarity NPC213178
0.5882 Remote Similarity NPC131892
0.5882 Remote Similarity NPC144511
0.5882 Remote Similarity NPC475062
0.5882 Remote Similarity NPC475952
0.5882 Remote Similarity NPC321732
0.5882 Remote Similarity NPC6120

  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 NPC13105 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
0.72 Intermediate Similarity NPD634 Phase 3
0.6939 Remote Similarity NPD387 Clinical (unspecified phase)
0.6786 Remote Similarity NPD615 Clinical (unspecified phase)
0.6667 Remote Similarity NPD2699 Approved
0.6596 Remote Similarity NPD9449 Clinical (unspecified phase)
0.6531 Remote Similarity NPD1460 Approved
0.65 Remote Similarity NPD3198 Approved
0.6491 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6429 Remote Similarity NPD3186 Phase 1
0.6349 Remote Similarity NPD7909 Approved
0.6275 Remote Similarity NPD1462 Approved
0.625 Remote Similarity NPD3171 Clinical (unspecified phase)
0.617 Remote Similarity NPD9447 Approved
0.6154 Remote Similarity NPD367 Approved
0.6122 Remote Similarity NPD3206 Approved
0.6 Remote Similarity NPD7341 Phase 2
0.6 Remote Similarity NPD2266 Phase 2
0.6 Remote Similarity NPD9448 Phase 2
0.6 Remote Similarity NPD77 Approved
0.6 Remote Similarity NPD633 Phase 3
0.6 Remote Similarity NPD6125 Clinical (unspecified phase)
0.6 Remote Similarity NPD9450 Approved
0.5942 Remote Similarity NPD5777 Approved
0.5926 Remote Similarity NPD388 Approved
0.5926 Remote Similarity NPD386 Approved
0.5915 Remote Similarity NPD3702 Approved
0.5882 Remote Similarity NPD3699 Clinical (unspecified phase)
0.5882 Remote Similarity NPD3698 Phase 2
0.5882 Remote Similarity NPD3700 Clinical (unspecified phase)
0.5818 Remote Similarity NPD343 Approved
0.5818 Remote Similarity NPD344 Approved
0.5818 Remote Similarity NPD345 Approved
0.5818 Remote Similarity NPD384 Approved
0.5818 Remote Similarity NPD385 Approved
0.5797 Remote Similarity NPD4244 Approved
0.5797 Remote Similarity NPD4789 Approved
0.5797 Remote Similarity NPD4245 Approved
0.5769 Remote Similarity NPD2270 Approved
0.5758 Remote Similarity NPD9496 Clinical (unspecified phase)
0.5735 Remote Similarity NPD229 Approved
0.5735 Remote Similarity NPD5360 Phase 3
0.5735 Remote Similarity NPD5361 Clinical (unspecified phase)
0.5714 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5714 Remote Similarity NPD4808 Clinical (unspecified phase)
0.5686 Remote Similarity NPD9655 Approved
0.5672 Remote Similarity NPD4224 Phase 2
0.5667 Remote Similarity NPD3728 Approved
0.5667 Remote Similarity NPD3730 Approved
0.5652 Remote Similarity NPD3726 Approved
0.5652 Remote Similarity NPD3725 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