Structure

Physi-Chem Properties

Molecular Weight:  182.13
Volume:  208.483
LogP:  3.145
LogD:  2.44
LogS:  -2.798
# Rotatable Bonds:  5
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.379
Synthetic Accessibility Score:  2.545
Fsp3:  0.545
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.4
MDCK Permeability:  2.5001134417834692e-05
Pgp-inhibitor:  0.633
Pgp-substrate:  0.014
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.269
30% Bioavailability (F30%):  0.143

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.971
Plasma Protein Binding (PPB):  90.99304962158203%
Volume Distribution (VD):  2.856
Pgp-substrate:  13.491107940673828%

ADMET: Metabolism

CYP1A2-inhibitor:  0.926
CYP1A2-substrate:  0.727
CYP2C19-inhibitor:  0.88
CYP2C19-substrate:  0.864
CYP2C9-inhibitor:  0.716
CYP2C9-substrate:  0.74
CYP2D6-inhibitor:  0.119
CYP2D6-substrate:  0.245
CYP3A4-inhibitor:  0.15
CYP3A4-substrate:  0.28

ADMET: Excretion

Clearance (CL):  8.027
Half-life (T1/2):  0.777

ADMET: Toxicity

hERG Blockers:  0.019
Human Hepatotoxicity (H-HT):  0.896
Drug-inuced Liver Injury (DILI):  0.037
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.011
Maximum Recommended Daily Dose:  0.042
Skin Sensitization:  0.947
Carcinogencity:  0.074
Eye Corrosion:  0.87
Eye Irritation:  0.921
Respiratory Toxicity:  0.134

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

  Natural Product: NPC270706

Natural Product ID:  NPC270706
Common Name*:   Methyl 3,7-Dimethylocta-2,6-Dienoate
IUPAC Name:   methyl 3,7-dimethylocta-2,6-dienoate
Synonyms:  
Standard InCHIKey:  ACOBBFVLNKYODD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H18O2/c1-9(2)6-5-7-10(3)8-11(12)13-4/h6,8H,5,7H2,1-4H3
SMILES:  CC(=CCCC(=CC(=O)OC)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3184963
PubChem CID:   70917
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001127] Acyclic monoterpenoids

*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
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[10336650]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[15679315]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[16252923]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[17624889]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18611049]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18768384]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[19476340]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[21912858]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[22111577]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. flower n.a. PMID[22166201]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota leaves n.a. n.a. PMID[22272932]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[23790907]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[24948953]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[25320841]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[25564559]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[29154541]
NPO15730 Citrus medica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15730 Citrus medica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15730 Citrus medica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15730 Citrus medica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15730 Citrus medica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota 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
NPT2 Others Unspecified Potency n.a. 245.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 54482.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 19493.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 3.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68589.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 24541.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 19331.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 194.9 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 NPC270706 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
0.9767 High Similarity NPC128280
0.913 High Similarity NPC236338
0.9091 High Similarity NPC26600
0.9091 High Similarity NPC47946
0.8889 High Similarity NPC197467
0.8511 High Similarity NPC135698
0.8444 Intermediate Similarity NPC304079
0.8444 Intermediate Similarity NPC6963
0.8444 Intermediate Similarity NPC12907
0.84 Intermediate Similarity NPC478120
0.8333 Intermediate Similarity NPC15789
0.8085 Intermediate Similarity NPC308331
0.8 Intermediate Similarity NPC57923
0.7925 Intermediate Similarity NPC294938
0.7925 Intermediate Similarity NPC135863
0.7925 Intermediate Similarity NPC249850
0.7925 Intermediate Similarity NPC129150
0.7925 Intermediate Similarity NPC293437
0.7885 Intermediate Similarity NPC478117
0.7778 Intermediate Similarity NPC254095
0.7778 Intermediate Similarity NPC223679
0.7778 Intermediate Similarity NPC21946
0.7755 Intermediate Similarity NPC15912
0.7636 Intermediate Similarity NPC286189
0.7636 Intermediate Similarity NPC82465
0.76 Intermediate Similarity NPC27264
0.75 Intermediate Similarity NPC79756
0.7451 Intermediate Similarity NPC148056
0.7407 Intermediate Similarity NPC245002
0.7407 Intermediate Similarity NPC221763
0.7407 Intermediate Similarity NPC96663
0.74 Intermediate Similarity NPC234084
0.74 Intermediate Similarity NPC91765
0.7368 Intermediate Similarity NPC151648
0.7358 Intermediate Similarity NPC159535
0.7358 Intermediate Similarity NPC151761
0.7308 Intermediate Similarity NPC191643
0.7308 Intermediate Similarity NPC106531
0.7308 Intermediate Similarity NPC151919
0.7255 Intermediate Similarity NPC275316
0.7241 Intermediate Similarity NPC155849
0.7241 Intermediate Similarity NPC44343
0.7241 Intermediate Similarity NPC210303
0.7241 Intermediate Similarity NPC179087
0.7241 Intermediate Similarity NPC217940
0.7241 Intermediate Similarity NPC68110
0.7222 Intermediate Similarity NPC173157
0.7174 Intermediate Similarity NPC18205
0.7174 Intermediate Similarity NPC297608
0.7174 Intermediate Similarity NPC12319
0.7091 Intermediate Similarity NPC150717
0.7037 Intermediate Similarity NPC474127
0.7037 Intermediate Similarity NPC269615
0.7037 Intermediate Similarity NPC218486
0.7021 Intermediate Similarity NPC221250
0.7018 Intermediate Similarity NPC159650
0.7018 Intermediate Similarity NPC133600
0.7018 Intermediate Similarity NPC22897
0.7 Intermediate Similarity NPC133904
0.7 Intermediate Similarity NPC282760
0.7 Intermediate Similarity NPC220766
0.7 Intermediate Similarity NPC182794
0.6949 Remote Similarity NPC473737
0.6949 Remote Similarity NPC474658
0.6923 Remote Similarity NPC289388
0.6909 Remote Similarity NPC474913
0.6909 Remote Similarity NPC49028
0.6897 Remote Similarity NPC309408
0.6897 Remote Similarity NPC26223
0.6897 Remote Similarity NPC19241
0.6885 Remote Similarity NPC191233
0.6885 Remote Similarity NPC185587
0.6885 Remote Similarity NPC248125
0.6875 Remote Similarity NPC187922
0.6852 Remote Similarity NPC477780
0.6852 Remote Similarity NPC477781
0.6842 Remote Similarity NPC474084
0.6809 Remote Similarity NPC250954
0.6809 Remote Similarity NPC281043
0.6809 Remote Similarity NPC123357
0.6809 Remote Similarity NPC8270
0.6792 Remote Similarity NPC43053
0.6792 Remote Similarity NPC244452
0.6786 Remote Similarity NPC86948
0.678 Remote Similarity NPC55376
0.678 Remote Similarity NPC26810
0.678 Remote Similarity NPC15193
0.6774 Remote Similarity NPC203335
0.6774 Remote Similarity NPC225272
0.6774 Remote Similarity NPC472266
0.6739 Remote Similarity NPC226511
0.6724 Remote Similarity NPC97570
0.6721 Remote Similarity NPC470123
0.6721 Remote Similarity NPC131174
0.6721 Remote Similarity NPC273600
0.6721 Remote Similarity NPC471566
0.6721 Remote Similarity NPC470688
0.6721 Remote Similarity NPC471556
0.6721 Remote Similarity NPC471565
0.6667 Remote Similarity NPC283502
0.6667 Remote Similarity NPC212730
0.6667 Remote Similarity NPC170167
0.6667 Remote Similarity NPC2328
0.6667 Remote Similarity NPC308418
0.6667 Remote Similarity NPC218477
0.6667 Remote Similarity NPC474823
0.6667 Remote Similarity NPC132243
0.6667 Remote Similarity NPC216407
0.6667 Remote Similarity NPC276290
0.6667 Remote Similarity NPC475073
0.6667 Remote Similarity NPC471279
0.6667 Remote Similarity NPC470256
0.6667 Remote Similarity NPC87137
0.6667 Remote Similarity NPC471277
0.6667 Remote Similarity NPC310210
0.6667 Remote Similarity NPC265551
0.6613 Remote Similarity NPC475555
0.6613 Remote Similarity NPC475675
0.6613 Remote Similarity NPC315115
0.661 Remote Similarity NPC130953
0.6604 Remote Similarity NPC221467
0.66 Remote Similarity NPC477686
0.66 Remote Similarity NPC312547
0.6596 Remote Similarity NPC182840
0.6596 Remote Similarity NPC29091
0.6596 Remote Similarity NPC103213
0.6596 Remote Similarity NPC255042
0.6591 Remote Similarity NPC12889
0.6562 Remote Similarity NPC151481
0.6562 Remote Similarity NPC232812
0.6562 Remote Similarity NPC88877
0.6562 Remote Similarity NPC476591
0.6562 Remote Similarity NPC475004
0.6562 Remote Similarity NPC470693
0.6557 Remote Similarity NPC148233
0.6557 Remote Similarity NPC25747
0.6557 Remote Similarity NPC34883
0.6557 Remote Similarity NPC226066
0.6557 Remote Similarity NPC308457
0.6557 Remote Similarity NPC329698
0.6552 Remote Similarity NPC189700
0.6552 Remote Similarity NPC471619
0.6552 Remote Similarity NPC478096
0.6522 Remote Similarity NPC185839
0.6508 Remote Similarity NPC194871
0.6508 Remote Similarity NPC132286
0.65 Remote Similarity NPC270412
0.65 Remote Similarity NPC14437
0.6491 Remote Similarity NPC324224
0.6491 Remote Similarity NPC472808
0.6471 Remote Similarity NPC191337
0.6462 Remote Similarity NPC315285
0.6462 Remote Similarity NPC469660
0.6462 Remote Similarity NPC37929
0.6462 Remote Similarity NPC64234
0.6462 Remote Similarity NPC59558
0.6458 Remote Similarity NPC111474
0.6458 Remote Similarity NPC101147
0.6452 Remote Similarity NPC19769
0.6452 Remote Similarity NPC96414
0.6441 Remote Similarity NPC222852
0.6441 Remote Similarity NPC478095
0.6441 Remote Similarity NPC302564
0.6441 Remote Similarity NPC474267
0.6429 Remote Similarity NPC154626
0.6429 Remote Similarity NPC189677
0.6415 Remote Similarity NPC267110
0.6415 Remote Similarity NPC234597
0.6415 Remote Similarity NPC207815
0.6406 Remote Similarity NPC238223
0.6406 Remote Similarity NPC287705
0.6406 Remote Similarity NPC477117
0.6406 Remote Similarity NPC313444
0.64 Remote Similarity NPC116934
0.64 Remote Similarity NPC301972
0.64 Remote Similarity NPC216921
0.6393 Remote Similarity NPC474774
0.6383 Remote Similarity NPC180840
0.6364 Remote Similarity NPC84038
0.6364 Remote Similarity NPC316185
0.6364 Remote Similarity NPC181587
0.6364 Remote Similarity NPC186531
0.6364 Remote Similarity NPC257618
0.6364 Remote Similarity NPC266979
0.6349 Remote Similarity NPC37382
0.6349 Remote Similarity NPC124586
0.6349 Remote Similarity NPC116013
0.6349 Remote Similarity NPC201356
0.6349 Remote Similarity NPC146811
0.6346 Remote Similarity NPC262558
0.6346 Remote Similarity NPC8610
0.6333 Remote Similarity NPC471278
0.6333 Remote Similarity NPC429928
0.6333 Remote Similarity NPC299730
0.6333 Remote Similarity NPC98519
0.6327 Remote Similarity NPC159773
0.6327 Remote Similarity NPC33489
0.6327 Remote Similarity NPC269823
0.6316 Remote Similarity NPC25038
0.6308 Remote Similarity NPC265574

  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 NPC270706 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
0.8163 Intermediate Similarity NPD6927 Phase 3
0.7755 Intermediate Similarity NPD4220 Pre-registration
0.7 Intermediate Similarity NPD2685 Clinical (unspecified phase)
0.6889 Remote Similarity NPD9115 Approved
0.6604 Remote Similarity NPD2268 Discontinued
0.66 Remote Similarity NPD6097 Approved
0.66 Remote Similarity NPD6096 Approved
0.6557 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6538 Remote Similarity NPD5343 Approved
0.65 Remote Similarity NPD9418 Clinical (unspecified phase)
0.64 Remote Similarity NPD9411 Phase 1
0.625 Remote Similarity NPD5783 Phase 3
0.623 Remote Similarity NPD4194 Approved
0.623 Remote Similarity NPD4191 Approved
0.623 Remote Similarity NPD4192 Approved
0.623 Remote Similarity NPD4193 Approved
0.6154 Remote Similarity NPD3174 Discontinued
0.6154 Remote Similarity NPD4222 Approved
0.6154 Remote Similarity NPD4265 Approved
0.6154 Remote Similarity NPD39 Approved
0.6087 Remote Similarity NPD1452 Discontinued
0.6078 Remote Similarity NPD5326 Phase 3
0.5909 Remote Similarity NPD9114 Clinical (unspecified phase)
0.5833 Remote Similarity NPD8779 Phase 3
0.5818 Remote Similarity NPD3173 Approved
0.5634 Remote Similarity NPD8039 Approved
0.5614 Remote Similarity NPD28 Approved
0.5614 Remote Similarity NPD29 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