Structure

Physi-Chem Properties

Molecular Weight:  206.17
Volume:  243.025
LogP:  3.947
LogD:  3.431
LogS:  -4.209
# Rotatable Bonds:  2
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.626
Synthetic Accessibility Score:  3.494
Fsp3:  0.643
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.59
MDCK Permeability:  2.6409697966300882e-05
Pgp-inhibitor:  0.983
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.061
30% Bioavailability (F30%):  0.012

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.098
Plasma Protein Binding (PPB):  95.81197357177734%
Volume Distribution (VD):  2.163
Pgp-substrate:  4.117232799530029%

ADMET: Metabolism

CYP1A2-inhibitor:  0.437
CYP1A2-substrate:  0.735
CYP2C19-inhibitor:  0.406
CYP2C19-substrate:  0.932
CYP2C9-inhibitor:  0.127
CYP2C9-substrate:  0.794
CYP2D6-inhibitor:  0.146
CYP2D6-substrate:  0.86
CYP3A4-inhibitor:  0.029
CYP3A4-substrate:  0.68

ADMET: Excretion

Clearance (CL):  2.231
Half-life (T1/2):  0.491

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.284
Drug-inuced Liver Injury (DILI):  0.173
AMES Toxicity:  0.021
Rat Oral Acute Toxicity:  0.092
Maximum Recommended Daily Dose:  0.758
Skin Sensitization:  0.855
Carcinogencity:  0.745
Eye Corrosion:  0.708
Eye Irritation:  0.868
Respiratory Toxicity:  0.973

Download Data

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

  Natural Product: NPC5626

Natural Product ID:  NPC5626
Common Name*:   (E)-4-(2,5,6,6-Tetramethylcyclohex-2-En-1-Yl)But-3-En-2-One
IUPAC Name:   (E)-4-(2,5,6,6-tetramethylcyclohex-2-en-1-yl)but-3-en-2-one
Synonyms:  
Standard InCHIKey:  JZQOJFLIJNRDHK-CMDGGOBGSA-N
Standard InCHI:  InChI=1S/C14H22O/c1-10-6-7-11(2)14(4,5)13(10)9-8-12(3)15/h6,8-9,11,13H,7H2,1-5H3/b9-8+
SMILES:  CC(=O)/C=C/C1C(=CCC(C1(C)C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3183603
PubChem CID:   5371002
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
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)94679-X]
NPO7478 Iris germanica Species Iridaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO7478 Iris germanica Species Iridaceae Eukaryota n.a. rhizome n.a. PMID[22388969]
NPO7478 Iris germanica Species Iridaceae Eukaryota n.a. rhizome n.a. PMID[25204177]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[30199256]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7478 Iris germanica Species Iridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7478 Iris germanica Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7478 Iris germanica Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22104 Trifolium pratense Species Fabaceae 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
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 61130.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 24336.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 48557.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 76958.8 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 NPC5626 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
0.98 High Similarity NPC14002
0.9412 High Similarity NPC23117
0.8909 High Similarity NPC311852
0.8571 High Similarity NPC60772
0.8333 Intermediate Similarity NPC295777
0.8333 Intermediate Similarity NPC69898
0.8246 Intermediate Similarity NPC170799
0.8246 Intermediate Similarity NPC308108
0.8197 Intermediate Similarity NPC92327
0.8197 Intermediate Similarity NPC176171
0.8113 Intermediate Similarity NPC163984
0.8113 Intermediate Similarity NPC58970
0.8113 Intermediate Similarity NPC176819
0.8065 Intermediate Similarity NPC176107
0.8033 Intermediate Similarity NPC251118
0.8 Intermediate Similarity NPC268564
0.8 Intermediate Similarity NPC288253
0.8 Intermediate Similarity NPC37644
0.7966 Intermediate Similarity NPC127582
0.7963 Intermediate Similarity NPC64866
0.7937 Intermediate Similarity NPC188292
0.7937 Intermediate Similarity NPC87141
0.7937 Intermediate Similarity NPC260474
0.7869 Intermediate Similarity NPC6697
0.7869 Intermediate Similarity NPC475124
0.7869 Intermediate Similarity NPC285371
0.7869 Intermediate Similarity NPC212210
0.7833 Intermediate Similarity NPC213152
0.7812 Intermediate Similarity NPC256846
0.7797 Intermediate Similarity NPC276764
0.7797 Intermediate Similarity NPC472304
0.7778 Intermediate Similarity NPC32351
0.7778 Intermediate Similarity NPC228776
0.7778 Intermediate Similarity NPC118788
0.7759 Intermediate Similarity NPC115385
0.7705 Intermediate Similarity NPC165695
0.7656 Intermediate Similarity NPC310992
0.7656 Intermediate Similarity NPC117804
0.7647 Intermediate Similarity NPC216921
0.7627 Intermediate Similarity NPC56905
0.7627 Intermediate Similarity NPC27610
0.7581 Intermediate Similarity NPC469662
0.7576 Intermediate Similarity NPC54123
0.75 Intermediate Similarity NPC475523
0.7463 Intermediate Similarity NPC470044
0.7463 Intermediate Similarity NPC470045
0.7463 Intermediate Similarity NPC251705
0.746 Intermediate Similarity NPC470329
0.7458 Intermediate Similarity NPC321568
0.7458 Intermediate Similarity NPC22019
0.7458 Intermediate Similarity NPC208749
0.7458 Intermediate Similarity NPC281986
0.7424 Intermediate Similarity NPC2634
0.7424 Intermediate Similarity NPC265782
0.7424 Intermediate Similarity NPC251929
0.7419 Intermediate Similarity NPC197238
0.7419 Intermediate Similarity NPC202118
0.7414 Intermediate Similarity NPC200258
0.7407 Intermediate Similarity NPC91962
0.7385 Intermediate Similarity NPC155198
0.7358 Intermediate Similarity NPC13991
0.7358 Intermediate Similarity NPC166788
0.7358 Intermediate Similarity NPC241784
0.7358 Intermediate Similarity NPC114239
0.7313 Intermediate Similarity NPC474562
0.7313 Intermediate Similarity NPC225467
0.7313 Intermediate Similarity NPC234707
0.7313 Intermediate Similarity NPC95863
0.7313 Intermediate Similarity NPC115023
0.7313 Intermediate Similarity NPC5701
0.7288 Intermediate Similarity NPC473733
0.7273 Intermediate Similarity NPC136473
0.7273 Intermediate Similarity NPC139397
0.7258 Intermediate Similarity NPC60565
0.7246 Intermediate Similarity NPC476346
0.7246 Intermediate Similarity NPC293803
0.7231 Intermediate Similarity NPC4370
0.7231 Intermediate Similarity NPC290350
0.7222 Intermediate Similarity NPC8610
0.7222 Intermediate Similarity NPC262558
0.7213 Intermediate Similarity NPC96551
0.7213 Intermediate Similarity NPC285594
0.7206 Intermediate Similarity NPC276336
0.7206 Intermediate Similarity NPC303613
0.7206 Intermediate Similarity NPC474228
0.72 Intermediate Similarity NPC217923
0.7164 Intermediate Similarity NPC307176
0.7164 Intermediate Similarity NPC159577
0.7164 Intermediate Similarity NPC35734
0.7164 Intermediate Similarity NPC282593
0.7164 Intermediate Similarity NPC260040
0.7143 Intermediate Similarity NPC1254
0.7143 Intermediate Similarity NPC32285
0.7143 Intermediate Similarity NPC474463
0.7143 Intermediate Similarity NPC69408
0.7101 Intermediate Similarity NPC474796
0.7101 Intermediate Similarity NPC329866
0.7101 Intermediate Similarity NPC309852
0.7101 Intermediate Similarity NPC474797
0.7097 Intermediate Similarity NPC25853
0.7091 Intermediate Similarity NPC124851
0.7077 Intermediate Similarity NPC259156
0.7077 Intermediate Similarity NPC323005
0.7077 Intermediate Similarity NPC242945
0.7069 Intermediate Similarity NPC296311
0.7059 Intermediate Similarity NPC190035
0.7059 Intermediate Similarity NPC305501
0.7049 Intermediate Similarity NPC266295
0.7049 Intermediate Similarity NPC94991
0.7049 Intermediate Similarity NPC30215
0.7037 Intermediate Similarity NPC296337
0.7037 Intermediate Similarity NPC86683
0.7037 Intermediate Similarity NPC191337
0.7031 Intermediate Similarity NPC52449
0.7031 Intermediate Similarity NPC169275
0.7031 Intermediate Similarity NPC4638
0.7015 Intermediate Similarity NPC182815
0.7 Intermediate Similarity NPC473171
0.6984 Remote Similarity NPC469728
0.6964 Remote Similarity NPC17518
0.6957 Remote Similarity NPC130016
0.6957 Remote Similarity NPC153660
0.6957 Remote Similarity NPC180015
0.6957 Remote Similarity NPC109576
0.6957 Remote Similarity NPC56747
0.6957 Remote Similarity NPC186042
0.6949 Remote Similarity NPC209431
0.6949 Remote Similarity NPC100809
0.6944 Remote Similarity NPC105197
0.6935 Remote Similarity NPC259261
0.6912 Remote Similarity NPC151045
0.6912 Remote Similarity NPC246722
0.6909 Remote Similarity NPC236355
0.6909 Remote Similarity NPC4079
0.6909 Remote Similarity NPC14917
0.6901 Remote Similarity NPC469796
0.6901 Remote Similarity NPC469793
0.6885 Remote Similarity NPC192427
0.6875 Remote Similarity NPC472306
0.6866 Remote Similarity NPC82477
0.6866 Remote Similarity NPC296697
0.6866 Remote Similarity NPC20610
0.6866 Remote Similarity NPC142754
0.6866 Remote Similarity NPC39157
0.6857 Remote Similarity NPC22134
0.6857 Remote Similarity NPC255021
0.6852 Remote Similarity NPC477686
0.6852 Remote Similarity NPC248411
0.6852 Remote Similarity NPC25771
0.6852 Remote Similarity NPC202189
0.6849 Remote Similarity NPC190211
0.6842 Remote Similarity NPC116906
0.6842 Remote Similarity NPC15325
0.6825 Remote Similarity NPC176621
0.6818 Remote Similarity NPC255781
0.6812 Remote Similarity NPC21944
0.6812 Remote Similarity NPC181204
0.6812 Remote Similarity NPC304983
0.6812 Remote Similarity NPC470078
0.68 Remote Similarity NPC34764
0.68 Remote Similarity NPC190810
0.68 Remote Similarity NPC76145
0.6792 Remote Similarity NPC105246
0.6792 Remote Similarity NPC190232
0.6765 Remote Similarity NPC286814
0.6761 Remote Similarity NPC255650
0.6761 Remote Similarity NPC65650
0.6757 Remote Similarity NPC476809
0.6757 Remote Similarity NPC474509
0.6731 Remote Similarity NPC183670
0.6731 Remote Similarity NPC111474
0.6724 Remote Similarity NPC26906
0.6724 Remote Similarity NPC214584
0.6724 Remote Similarity NPC236623
0.6724 Remote Similarity NPC27438
0.6721 Remote Similarity NPC141699
0.6719 Remote Similarity NPC475795
0.6719 Remote Similarity NPC329416
0.6719 Remote Similarity NPC317177
0.6719 Remote Similarity NPC294304
0.6719 Remote Similarity NPC326645
0.6719 Remote Similarity NPC97322
0.6719 Remote Similarity NPC317025
0.6719 Remote Similarity NPC228574
0.6716 Remote Similarity NPC20181
0.6716 Remote Similarity NPC220210
0.6714 Remote Similarity NPC201562
0.6714 Remote Similarity NPC29542
0.6714 Remote Similarity NPC323437
0.6712 Remote Similarity NPC189485
0.6712 Remote Similarity NPC74410
0.6712 Remote Similarity NPC275494
0.6712 Remote Similarity NPC471409
0.6712 Remote Similarity NPC115515
0.6667 Remote Similarity NPC192529
0.6667 Remote Similarity NPC139717
0.6667 Remote Similarity NPC112680
0.6667 Remote Similarity NPC292463
0.6667 Remote Similarity NPC107258
0.6667 Remote Similarity NPC475833

  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 NPC5626 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
0.8246 Intermediate Similarity NPD287 Approved
0.7424 Intermediate Similarity NPD4691 Approved
0.7353 Intermediate Similarity NPD4058 Approved
0.7273 Intermediate Similarity NPD4137 Phase 3
0.7164 Intermediate Similarity NPD4747 Approved
0.7101 Intermediate Similarity NPD4687 Approved
0.6866 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6857 Remote Similarity NPD5733 Approved
0.6849 Remote Similarity NPD4195 Approved
0.6812 Remote Similarity NPD5276 Approved
0.68 Remote Similarity NPD319 Phase 1
0.6792 Remote Similarity NPD1799 Clinical (unspecified phase)
0.6719 Remote Similarity NPD4194 Approved
0.6719 Remote Similarity NPD4192 Approved
0.6719 Remote Similarity NPD4191 Approved
0.6719 Remote Similarity NPD4193 Approved
0.6494 Remote Similarity NPD3527 Clinical (unspecified phase)
0.6316 Remote Similarity NPD4695 Discontinued
0.625 Remote Similarity NPD5690 Phase 2
0.6234 Remote Similarity NPD8028 Phase 2
0.619 Remote Similarity NPD4219 Approved
0.6173 Remote Similarity NPD3573 Approved
0.6154 Remote Similarity NPD4223 Phase 3
0.6154 Remote Similarity NPD4221 Approved
0.6102 Remote Similarity NPD8262 Approved
0.6049 Remote Similarity NPD4623 Approved
0.6049 Remote Similarity NPD4519 Discontinued
0.6029 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6 Remote Similarity NPD4197 Approved
0.6 Remote Similarity NPD3665 Phase 1
0.6 Remote Similarity NPD3666 Approved
0.6 Remote Similarity NPD3133 Approved
0.5946 Remote Similarity NPD4785 Approved
0.5946 Remote Similarity NPD4784 Approved
0.5926 Remote Similarity NPD5329 Approved
0.5926 Remote Similarity NPD5783 Phase 3
0.589 Remote Similarity NPD4243 Approved
0.5882 Remote Similarity NPD6079 Approved
0.5857 Remote Similarity NPD7331 Phase 2
0.5854 Remote Similarity NPD5330 Approved
0.5854 Remote Similarity NPD7146 Approved
0.5854 Remote Similarity NPD4693 Phase 3
0.5854 Remote Similarity NPD4694 Approved
0.5854 Remote Similarity NPD3618 Phase 1
0.5854 Remote Similarity NPD7521 Approved
0.5854 Remote Similarity NPD6409 Approved
0.5854 Remote Similarity NPD3574 Clinical (unspecified phase)
0.5854 Remote Similarity NPD6684 Approved
0.5854 Remote Similarity NPD4689 Approved
0.5854 Remote Similarity NPD4688 Approved
0.5854 Remote Similarity NPD7334 Approved
0.5854 Remote Similarity NPD5205 Approved
0.5854 Remote Similarity NPD5280 Approved
0.5854 Remote Similarity NPD4138 Approved
0.5854 Remote Similarity NPD4690 Approved
0.5844 Remote Similarity NPD3617 Approved
0.5781 Remote Similarity NPD342 Phase 1
0.5765 Remote Similarity NPD5207 Approved
0.575 Remote Similarity NPD3667 Approved
0.5735 Remote Similarity NPD368 Approved
0.5732 Remote Similarity NPD1696 Phase 3
0.5732 Remote Similarity NPD1694 Approved
0.5714 Remote Similarity NPD7513 Clinical (unspecified phase)
0.5714 Remote Similarity NPD5737 Approved
0.5714 Remote Similarity NPD6672 Approved
0.5714 Remote Similarity NPD6903 Approved
0.5714 Remote Similarity NPD5208 Approved
0.5698 Remote Similarity NPD5284 Approved
0.5698 Remote Similarity NPD5694 Approved
0.5698 Remote Similarity NPD5281 Approved
0.5696 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5682 Remote Similarity NPD5210 Approved
0.5682 Remote Similarity NPD4629 Approved
0.5663 Remote Similarity NPD5279 Phase 3
0.5658 Remote Similarity NPD7339 Approved
0.5658 Remote Similarity NPD8264 Approved
0.5658 Remote Similarity NPD6942 Approved
0.5658 Remote Similarity NPD5275 Approved
0.5658 Remote Similarity NPD4190 Phase 3
0.5647 Remote Similarity NPD5328 Approved
0.5647 Remote Similarity NPD4753 Phase 2
0.5647 Remote Similarity NPD6673 Approved
0.5647 Remote Similarity NPD6904 Approved
0.5647 Remote Similarity NPD6080 Approved
0.5634 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5618 Remote Similarity NPD5222 Approved
0.5618 Remote Similarity NPD5221 Approved
0.5618 Remote Similarity NPD5220 Clinical (unspecified phase)
0.561 Remote Similarity NPD3668 Phase 3
0.561 Remote Similarity NPD4786 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