Structure

Physi-Chem Properties

Molecular Weight:  250.19
Volume:  292.327
LogP:  4.681
LogD:  4.111
LogS:  -4.573
# Rotatable Bonds:  8
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.375
Synthetic Accessibility Score:  2.735
Fsp3:  0.562
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:  -4.541
MDCK Permeability:  2.6787445676745847e-05
Pgp-inhibitor:  0.95
Pgp-substrate:  0.021
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  0.702
30% Bioavailability (F30%):  0.092

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.844
Plasma Protein Binding (PPB):  97.92810821533203%
Volume Distribution (VD):  3.507
Pgp-substrate:  5.064598560333252%

ADMET: Metabolism

CYP1A2-inhibitor:  0.951
CYP1A2-substrate:  0.532
CYP2C19-inhibitor:  0.814
CYP2C19-substrate:  0.821
CYP2C9-inhibitor:  0.905
CYP2C9-substrate:  0.908
CYP2D6-inhibitor:  0.446
CYP2D6-substrate:  0.209
CYP3A4-inhibitor:  0.547
CYP3A4-substrate:  0.222

ADMET: Excretion

Clearance (CL):  5.57
Half-life (T1/2):  0.593

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.885
Drug-inuced Liver Injury (DILI):  0.024
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.175
Skin Sensitization:  0.967
Carcinogencity:  0.037
Eye Corrosion:  0.677
Eye Irritation:  0.84
Respiratory Toxicity:  0.04

Download Data

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

  Natural Product: NPC128280

Natural Product ID:  NPC128280
Common Name*:   Methyl (2E,6E)-3,7,11-Trimethyldodeca-2,6,10-Trienoate
IUPAC Name:   methyl (2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoate
Synonyms:  
Standard InCHIKey:  NWKXNIPBVLQYAB-VDQVFBMKSA-N
Standard InCHI:  InChI=1S/C16H26O2/c1-13(2)8-6-9-14(3)10-7-11-15(4)12-16(17)18-5/h8,10,12H,6-7,9,11H2,1-5H3/b14-10+,15-12+
SMILES:  CC(=CCC/C(=C/CC/C(=C/C(=O)OC)/C)/C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL171329
PubChem CID:   5275508
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

*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
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota Flowers Tantempango, Hidalgo, Mexico 2019-May DOI[10.1007/s11130-020-00822-2]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[16297615]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. whole plant n.a. PMID[18543151]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[24358188]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[8778246]
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO9325 Dalbergia volubilis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9325 Dalbergia volubilis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11889 Dendrobium chrysanthum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11889 Dendrobium chrysanthum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3189 Polypodium japonicum Species Polypodiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9325 Dalbergia volubilis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11889 Dendrobium chrysanthum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11578 Aloe vera Species Xanthorrhoeaceae 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
NPT20 Organism Candida albicans Candida albicans IC50 > 100.0 ug.mL-1 PMID[533882]

☑ 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 NPC128280 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 NPC270706
0.9111 High Similarity NPC197467
0.8936 High Similarity NPC236338
0.8889 High Similarity NPC26600
0.8889 High Similarity NPC47946
0.8333 Intermediate Similarity NPC135698
0.8298 Intermediate Similarity NPC308331
0.8261 Intermediate Similarity NPC304079
0.8261 Intermediate Similarity NPC12907
0.8261 Intermediate Similarity NPC6963
0.8235 Intermediate Similarity NPC478120
0.8163 Intermediate Similarity NPC15789
0.8113 Intermediate Similarity NPC129150
0.8113 Intermediate Similarity NPC135863
0.8113 Intermediate Similarity NPC293437
0.8113 Intermediate Similarity NPC294938
0.8113 Intermediate Similarity NPC249850
0.7963 Intermediate Similarity NPC254095
0.7963 Intermediate Similarity NPC223679
0.7963 Intermediate Similarity NPC21946
0.7826 Intermediate Similarity NPC57923
0.7818 Intermediate Similarity NPC82465
0.7736 Intermediate Similarity NPC478117
0.7679 Intermediate Similarity NPC79756
0.76 Intermediate Similarity NPC15912
0.7593 Intermediate Similarity NPC245002
0.7593 Intermediate Similarity NPC96663
0.7547 Intermediate Similarity NPC151761
0.7547 Intermediate Similarity NPC159535
0.7544 Intermediate Similarity NPC151648
0.75 Intermediate Similarity NPC286189
0.75 Intermediate Similarity NPC106531
0.7451 Intermediate Similarity NPC27264
0.7414 Intermediate Similarity NPC44343
0.7414 Intermediate Similarity NPC155849
0.7414 Intermediate Similarity NPC210303
0.7414 Intermediate Similarity NPC217940
0.7414 Intermediate Similarity NPC68110
0.7414 Intermediate Similarity NPC179087
0.7308 Intermediate Similarity NPC148056
0.7273 Intermediate Similarity NPC221763
0.7255 Intermediate Similarity NPC91765
0.7255 Intermediate Similarity NPC234084
0.7222 Intermediate Similarity NPC269615
0.717 Intermediate Similarity NPC191643
0.717 Intermediate Similarity NPC151919
0.7167 Intermediate Similarity NPC220766
0.7167 Intermediate Similarity NPC282760
0.7115 Intermediate Similarity NPC275316
0.7091 Intermediate Similarity NPC173157
0.7091 Intermediate Similarity NPC474913
0.7069 Intermediate Similarity NPC26223
0.7049 Intermediate Similarity NPC185587
0.7049 Intermediate Similarity NPC191233
0.7049 Intermediate Similarity NPC248125
0.7037 Intermediate Similarity NPC477780
0.7037 Intermediate Similarity NPC477781
0.7021 Intermediate Similarity NPC18205
0.7021 Intermediate Similarity NPC297608
0.7021 Intermediate Similarity NPC12319
0.7018 Intermediate Similarity NPC474084
0.6981 Remote Similarity NPC43053
0.6964 Remote Similarity NPC150717
0.6949 Remote Similarity NPC55376
0.6949 Remote Similarity NPC26810
0.6935 Remote Similarity NPC203335
0.6935 Remote Similarity NPC225272
0.6935 Remote Similarity NPC472266
0.6909 Remote Similarity NPC218486
0.6909 Remote Similarity NPC474127
0.6897 Remote Similarity NPC159650
0.6897 Remote Similarity NPC133600
0.6897 Remote Similarity NPC22897
0.6885 Remote Similarity NPC133904
0.6885 Remote Similarity NPC471565
0.6885 Remote Similarity NPC471556
0.6885 Remote Similarity NPC471566
0.6885 Remote Similarity NPC182794
0.6885 Remote Similarity NPC470688
0.6875 Remote Similarity NPC221250
0.6842 Remote Similarity NPC265551
0.6842 Remote Similarity NPC283502
0.6842 Remote Similarity NPC471279
0.6842 Remote Similarity NPC212730
0.6842 Remote Similarity NPC471277
0.6833 Remote Similarity NPC473737
0.6833 Remote Similarity NPC474658
0.6825 Remote Similarity NPC218477
0.6825 Remote Similarity NPC276290
0.6825 Remote Similarity NPC470256
0.68 Remote Similarity NPC477686
0.6792 Remote Similarity NPC289388
0.6786 Remote Similarity NPC49028
0.678 Remote Similarity NPC19241
0.678 Remote Similarity NPC309408
0.6735 Remote Similarity NPC187922
0.6724 Remote Similarity NPC478096
0.6721 Remote Similarity NPC148233
0.6721 Remote Similarity NPC226066
0.6721 Remote Similarity NPC25747
0.6721 Remote Similarity NPC34883
0.6721 Remote Similarity NPC329698
0.6721 Remote Similarity NPC308457
0.6719 Remote Similarity NPC476591
0.6719 Remote Similarity NPC151481
0.6719 Remote Similarity NPC470693
0.6719 Remote Similarity NPC88877
0.6719 Remote Similarity NPC232812
0.6667 Remote Similarity NPC281043
0.6667 Remote Similarity NPC244452
0.6667 Remote Similarity NPC8270
0.6667 Remote Similarity NPC250954
0.6667 Remote Similarity NPC15193
0.6667 Remote Similarity NPC86948
0.6667 Remote Similarity NPC123357
0.6667 Remote Similarity NPC191337
0.6667 Remote Similarity NPC194871
0.6615 Remote Similarity NPC37929
0.6615 Remote Similarity NPC59558
0.6615 Remote Similarity NPC469660
0.6615 Remote Similarity NPC64234
0.6613 Remote Similarity NPC470123
0.6613 Remote Similarity NPC273600
0.6613 Remote Similarity NPC131174
0.661 Remote Similarity NPC478095
0.661 Remote Similarity NPC222852
0.661 Remote Similarity NPC97570
0.661 Remote Similarity NPC474267
0.6604 Remote Similarity NPC207815
0.6604 Remote Similarity NPC267110
0.66 Remote Similarity NPC116934
0.6596 Remote Similarity NPC180840
0.6596 Remote Similarity NPC226511
0.6562 Remote Similarity NPC474823
0.6562 Remote Similarity NPC310210
0.6557 Remote Similarity NPC475073
0.6557 Remote Similarity NPC2328
0.6557 Remote Similarity NPC132243
0.6545 Remote Similarity NPC216407
0.6545 Remote Similarity NPC170167
0.6538 Remote Similarity NPC87137
0.6538 Remote Similarity NPC262558
0.6538 Remote Similarity NPC8610
0.6531 Remote Similarity NPC269823
0.6522 Remote Similarity NPC308418
0.6515 Remote Similarity NPC84038
0.6515 Remote Similarity NPC257618
0.6515 Remote Similarity NPC181587
0.6515 Remote Similarity NPC316185
0.6515 Remote Similarity NPC186531
0.6508 Remote Similarity NPC124586
0.6508 Remote Similarity NPC146811
0.6508 Remote Similarity NPC475675
0.6508 Remote Similarity NPC315115
0.6508 Remote Similarity NPC475555
0.65 Remote Similarity NPC471278
0.65 Remote Similarity NPC130953
0.65 Remote Similarity NPC299730
0.6481 Remote Similarity NPC288381
0.6481 Remote Similarity NPC225974
0.6481 Remote Similarity NPC221467
0.6481 Remote Similarity NPC20934
0.6471 Remote Similarity NPC312547
0.6462 Remote Similarity NPC265574
0.6462 Remote Similarity NPC475004
0.6458 Remote Similarity NPC255042
0.6458 Remote Similarity NPC29091
0.6458 Remote Similarity NPC182840
0.6458 Remote Similarity NPC103213
0.6444 Remote Similarity NPC12889
0.6441 Remote Similarity NPC189700
0.6441 Remote Similarity NPC471619
0.6418 Remote Similarity NPC476489
0.6418 Remote Similarity NPC474705
0.6418 Remote Similarity NPC16349
0.6418 Remote Similarity NPC276336
0.6418 Remote Similarity NPC476490
0.6418 Remote Similarity NPC222244
0.6418 Remote Similarity NPC287878
0.6406 Remote Similarity NPC132286
0.6406 Remote Similarity NPC21998
0.64 Remote Similarity NPC213538
0.64 Remote Similarity NPC256766
0.6393 Remote Similarity NPC14437
0.6393 Remote Similarity NPC326645
0.6393 Remote Similarity NPC317025
0.6393 Remote Similarity NPC329416
0.6393 Remote Similarity NPC317177
0.6393 Remote Similarity NPC270412
0.6383 Remote Similarity NPC185839
0.6379 Remote Similarity NPC472808
0.6379 Remote Similarity NPC324224
0.6364 Remote Similarity NPC315285
0.6364 Remote Similarity NPC67183
0.6349 Remote Similarity NPC96414
0.6349 Remote Similarity NPC19769
0.6346 Remote Similarity NPC160628
0.6346 Remote Similarity NPC117572
0.6346 Remote Similarity NPC140501
0.6333 Remote Similarity NPC302564

  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 NPC128280 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
0.8367 Intermediate Similarity NPD6927 Phase 3
0.7959 Intermediate Similarity NPD4220 Pre-registration
0.7167 Intermediate Similarity NPD2685 Clinical (unspecified phase)
0.68 Remote Similarity NPD6096 Approved
0.68 Remote Similarity NPD6097 Approved
0.6792 Remote Similarity NPD2268 Discontinued
0.6739 Remote Similarity NPD9115 Approved
0.6731 Remote Similarity NPD5343 Approved
0.6721 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6458 Remote Similarity NPD5783 Phase 3
0.6393 Remote Similarity NPD9418 Clinical (unspecified phase)
0.6393 Remote Similarity NPD4192 Approved
0.6393 Remote Similarity NPD4193 Approved
0.6393 Remote Similarity NPD4194 Approved
0.6393 Remote Similarity NPD4191 Approved
0.6346 Remote Similarity NPD39 Approved
0.6346 Remote Similarity NPD4222 Approved
0.6346 Remote Similarity NPD3174 Discontinued
0.6346 Remote Similarity NPD4265 Approved
0.6275 Remote Similarity NPD5326 Phase 3
0.6275 Remote Similarity NPD9411 Phase 1
0.6 Remote Similarity NPD8779 Phase 3
0.6 Remote Similarity NPD3173 Approved
0.6 Remote Similarity NPD1452 Discontinued
0.5789 Remote Similarity NPD29 Approved
0.5789 Remote Similarity NPD28 Approved
0.5778 Remote Similarity NPD9114 Clinical (unspecified phase)
0.5775 Remote Similarity NPD8039 Approved
0.5714 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5658 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5658 Remote Similarity NPD5209 Approved
0.5645 Remote Similarity NPD6109 Phase 1
0.5616 Remote Similarity NPD4756 Discovery

  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