Structure

Physi-Chem Properties

Molecular Weight:  404.26
Volume:  449.156
LogP:  4.484
LogD:  3.895
LogS:  -4.226
# Rotatable Bonds:  15
TPSA:  83.83
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.233
Synthetic Accessibility Score:  3.177
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -5.132
MDCK Permeability:  2.3838572815293446e-05
Pgp-inhibitor:  0.076
Pgp-substrate:  0.76
Human Intestinal Absorption (HIA):  0.933
20% Bioavailability (F20%):  0.258
30% Bioavailability (F30%):  0.08

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.036
Plasma Protein Binding (PPB):  85.51025390625%
Volume Distribution (VD):  0.601
Pgp-substrate:  2.326718330383301%

ADMET: Metabolism

CYP1A2-inhibitor:  0.206
CYP1A2-substrate:  0.087
CYP2C19-inhibitor:  0.044
CYP2C19-substrate:  0.051
CYP2C9-inhibitor:  0.656
CYP2C9-substrate:  0.982
CYP2D6-inhibitor:  0.877
CYP2D6-substrate:  0.426
CYP3A4-inhibitor:  0.077
CYP3A4-substrate:  0.07

ADMET: Excretion

Clearance (CL):  2.701
Half-life (T1/2):  0.855

ADMET: Toxicity

hERG Blockers:  0.0
Human Hepatotoxicity (H-HT):  0.298
Drug-inuced Liver Injury (DILI):  0.008
AMES Toxicity:  0.0
Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.587
Skin Sensitization:  0.988
Carcinogencity:  0.008
Eye Corrosion:  0.706
Eye Irritation:  0.869
Respiratory Toxicity:  0.07

Download Data

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

  Natural Product: NPC223675

Natural Product ID:  NPC223675
Common Name*:   Dodecyl 2-Methylprop-2-Enoate
IUPAC Name:   dodecyl 2-methylprop-2-enoate
Synonyms:  
Standard InCHIKey:  GMSCBRSQMRDRCD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H30O2/c1-4-5-6-7-8-9-10-11-12-13-14-18-16(17)15(2)3/h2,4-14H2,1,3H3
SMILES:  CCCCCCCCCCCCOC(=O)C(=C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1903701
PubChem CID:   8906
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001722] Fatty alcohol esters

*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
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[1402962]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Flower Buds n.a. n.a. PMID[26977531]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[8904847]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3987 Syzygium aromaticum Species Myrtaceae 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
NPT108 Individual Protein Estrogen receptor alpha Homo sapiens Potency n.a. 25118.9 nM PMID[459995]
NPT540 Individual Protein Bile acid receptor FXR Homo sapiens Potency n.a. 1.0 nM PMID[459995]
NPT198 Individual Protein Vitamin D receptor Homo sapiens Potency n.a. 22387.2 nM PMID[459995]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 20000.0 nM PMID[459996]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 19952.62 nM PMID[459996]
NPT2 Others Unspecified Potency n.a. 68938.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 77350.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 21875.1 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 24544.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 24460.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 6113.1 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 NPC223675 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
0.9778 High Similarity NPC68577
0.9111 High Similarity NPC312547
0.7885 Intermediate Similarity NPC310746
0.7647 Intermediate Similarity NPC250919
0.7414 Intermediate Similarity NPC45097
0.74 Intermediate Similarity NPC172042
0.7292 Intermediate Similarity NPC159773
0.7174 Intermediate Similarity NPC128996
0.717 Intermediate Similarity NPC142103
0.7143 Intermediate Similarity NPC218477
0.7111 Intermediate Similarity NPC223374
0.7111 Intermediate Similarity NPC196442
0.7111 Intermediate Similarity NPC86545
0.7111 Intermediate Similarity NPC301398
0.6981 Remote Similarity NPC207815
0.6957 Remote Similarity NPC80641
0.6923 Remote Similarity NPC469660
0.6889 Remote Similarity NPC286498
0.6852 Remote Similarity NPC236338
0.6825 Remote Similarity NPC248125
0.6818 Remote Similarity NPC186531
0.6818 Remote Similarity NPC84038
0.68 Remote Similarity NPC236579
0.68 Remote Similarity NPC203531
0.6739 Remote Similarity NPC155872
0.6735 Remote Similarity NPC165533
0.6735 Remote Similarity NPC256163
0.6735 Remote Similarity NPC149299
0.6735 Remote Similarity NPC250028
0.6735 Remote Similarity NPC40597
0.6719 Remote Similarity NPC472266
0.6716 Remote Similarity NPC474705
0.6667 Remote Similarity NPC474267
0.6667 Remote Similarity NPC135698
0.6667 Remote Similarity NPC159650
0.6667 Remote Similarity NPC22897
0.6667 Remote Similarity NPC322892
0.6615 Remote Similarity NPC276290
0.6613 Remote Similarity NPC210303
0.6613 Remote Similarity NPC179087
0.6613 Remote Similarity NPC217940
0.6613 Remote Similarity NPC44343
0.6604 Remote Similarity NPC197467
0.66 Remote Similarity NPC53541
0.6596 Remote Similarity NPC65353
0.6567 Remote Similarity NPC163003
0.6557 Remote Similarity NPC79756
0.6557 Remote Similarity NPC143857
0.6557 Remote Similarity NPC299730
0.6557 Remote Similarity NPC229252
0.6552 Remote Similarity NPC223677
0.6552 Remote Similarity NPC128061
0.6552 Remote Similarity NPC28779
0.6552 Remote Similarity NPC10316
0.6552 Remote Similarity NPC200845
0.6545 Remote Similarity NPC15789
0.6538 Remote Similarity NPC51329
0.6538 Remote Similarity NPC47363
0.6538 Remote Similarity NPC287231
0.6531 Remote Similarity NPC80234
0.6531 Remote Similarity NPC223249
0.6522 Remote Similarity NPC154396
0.6522 Remote Similarity NPC469414
0.6522 Remote Similarity NPC329826
0.6515 Remote Similarity NPC265574
0.6515 Remote Similarity NPC475004
0.6508 Remote Similarity NPC34883
0.6491 Remote Similarity NPC71761
0.6481 Remote Similarity NPC216130
0.6462 Remote Similarity NPC194871
0.6458 Remote Similarity NPC14608
0.6452 Remote Similarity NPC151648
0.6444 Remote Similarity NPC40965
0.6441 Remote Similarity NPC96663
0.6429 Remote Similarity NPC244452
0.6415 Remote Similarity NPC47946
0.6415 Remote Similarity NPC26600
0.6406 Remote Similarity NPC182794
0.64 Remote Similarity NPC28598
0.64 Remote Similarity NPC161097
0.64 Remote Similarity NPC12156
0.6393 Remote Similarity NPC286189
0.6377 Remote Similarity NPC476355
0.6377 Remote Similarity NPC140287
0.6364 Remote Similarity NPC474823
0.6364 Remote Similarity NPC475760
0.6364 Remote Similarity NPC470256
0.6349 Remote Similarity NPC155849
0.6349 Remote Similarity NPC68110
0.6346 Remote Similarity NPC317128
0.6346 Remote Similarity NPC40805
0.6338 Remote Similarity NPC476794
0.6338 Remote Similarity NPC470240
0.6333 Remote Similarity NPC293437
0.6333 Remote Similarity NPC249850
0.6333 Remote Similarity NPC135863
0.6327 Remote Similarity NPC316546
0.6327 Remote Similarity NPC22903
0.6327 Remote Similarity NPC201622
0.6327 Remote Similarity NPC305660
0.6327 Remote Similarity NPC54980
0.6324 Remote Similarity NPC257618
0.6316 Remote Similarity NPC161366
0.6316 Remote Similarity NPC170167
0.6296 Remote Similarity NPC128280
0.6296 Remote Similarity NPC249754
0.6286 Remote Similarity NPC155587
0.6286 Remote Similarity NPC138408
0.6286 Remote Similarity NPC226669
0.6286 Remote Similarity NPC193351
0.6269 Remote Similarity NPC232812
0.6269 Remote Similarity NPC101622
0.6269 Remote Similarity NPC269841
0.625 Remote Similarity NPC289388
0.625 Remote Similarity NPC128276
0.625 Remote Similarity NPC80396
0.625 Remote Similarity NPC154642
0.6232 Remote Similarity NPC58956
0.6232 Remote Similarity NPC135703
0.6232 Remote Similarity NPC269206
0.6232 Remote Similarity NPC295633
0.623 Remote Similarity NPC21946
0.623 Remote Similarity NPC240206
0.623 Remote Similarity NPC254095
0.6212 Remote Similarity NPC225272
0.6212 Remote Similarity NPC21998
0.6212 Remote Similarity NPC203335
0.6207 Remote Similarity NPC39633
0.6207 Remote Similarity NPC309606
0.6207 Remote Similarity NPC139545
0.62 Remote Similarity NPC81263
0.62 Remote Similarity NPC31551
0.62 Remote Similarity NPC219536
0.6197 Remote Similarity NPC235906
0.6197 Remote Similarity NPC123360
0.6176 Remote Similarity NPC4299
0.6176 Remote Similarity NPC64234
0.6176 Remote Similarity NPC67183
0.6176 Remote Similarity NPC37929
0.617 Remote Similarity NPC63354
0.6164 Remote Similarity NPC617
0.6164 Remote Similarity NPC19841
0.6154 Remote Similarity NPC470688
0.6143 Remote Similarity NPC477204
0.6143 Remote Similarity NPC117746
0.6143 Remote Similarity NPC15499
0.6143 Remote Similarity NPC474758
0.6143 Remote Similarity NPC320537
0.6143 Remote Similarity NPC259599
0.6143 Remote Similarity NPC143979
0.6143 Remote Similarity NPC294434
0.6129 Remote Similarity NPC82465
0.6111 Remote Similarity NPC65603
0.6111 Remote Similarity NPC41780
0.6111 Remote Similarity NPC270706
0.6111 Remote Similarity NPC475711
0.6111 Remote Similarity NPC57744
0.6111 Remote Similarity NPC30195
0.6111 Remote Similarity NPC105329
0.6111 Remote Similarity NPC308301
0.6111 Remote Similarity NPC320630
0.6111 Remote Similarity NPC63182
0.6111 Remote Similarity NPC52700
0.6111 Remote Similarity NPC12438
0.6111 Remote Similarity NPC97516
0.6111 Remote Similarity NPC187568
0.6111 Remote Similarity NPC141789
0.6111 Remote Similarity NPC476028
0.6111 Remote Similarity NPC116177
0.6111 Remote Similarity NPC145045
0.6111 Remote Similarity NPC171204
0.6111 Remote Similarity NPC7563
0.6102 Remote Similarity NPC478120
0.6102 Remote Similarity NPC269615
0.6094 Remote Similarity NPC474658
0.6087 Remote Similarity NPC12904
0.6087 Remote Similarity NPC475762
0.6087 Remote Similarity NPC477084
0.6081 Remote Similarity NPC474510
0.6081 Remote Similarity NPC474981
0.6081 Remote Similarity NPC233377
0.6078 Remote Similarity NPC281043
0.6071 Remote Similarity NPC163345
0.6071 Remote Similarity NPC26253
0.6066 Remote Similarity NPC294938
0.6066 Remote Similarity NPC129150
0.6061 Remote Similarity NPC284447
0.6056 Remote Similarity NPC244166
0.6056 Remote Similarity NPC228978
0.6056 Remote Similarity NPC329852
0.6034 Remote Similarity NPC106531
0.6032 Remote Similarity NPC19241
0.6032 Remote Similarity NPC26223
0.6029 Remote Similarity NPC151481
0.6027 Remote Similarity NPC471220
0.6027 Remote Similarity NPC93763
0.6027 Remote Similarity NPC108816
0.6027 Remote Similarity NPC267231
0.6 Remote Similarity NPC228473
0.6 Remote Similarity NPC281949

  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 NPC223675 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
0.7895 Intermediate Similarity NPD3205 Discontinued
0.6731 Remote Similarity NPD9378 Approved
0.6727 Remote Similarity NPD6927 Phase 3
0.6667 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6538 Remote Similarity NPD2699 Approved
0.625 Remote Similarity NPD9437 Clinical (unspecified phase)
0.6056 Remote Similarity NPD8039 Approved
0.6 Remote Similarity NPD3206 Approved
0.5921 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5893 Remote Similarity NPD6125 Clinical (unspecified phase)
0.5893 Remote Similarity NPD5343 Approved
0.5862 Remote Similarity NPD28 Approved
0.5862 Remote Similarity NPD29 Approved
0.5769 Remote Similarity NPD8839 Phase 3
0.5758 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5714 Remote Similarity NPD5209 Approved
0.5667 Remote Similarity NPD3172 Approved
0.566 Remote Similarity NPD2270 Approved
0.5636 Remote Similarity NPD6097 Approved
0.5636 Remote Similarity NPD6096 Approved
0.5614 Remote Similarity NPD2266 Phase 2
0.5614 Remote Similarity NPD622 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