Structure

Physi-Chem Properties

Molecular Weight:  164.08
Volume:  179.994
LogP:  1.799
LogD:  0.827
LogS:  -2.52
# Rotatable Bonds:  1
TPSA:  34.14
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.436
Synthetic Accessibility Score:  3.101
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.437
MDCK Permeability:  2.0213039533700794e-05
Pgp-inhibitor:  0.126
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.016
30% Bioavailability (F30%):  0.011

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.064
Plasma Protein Binding (PPB):  91.55020904541016%
Volume Distribution (VD):  1.971
Pgp-substrate:  7.436884880065918%

ADMET: Metabolism

CYP1A2-inhibitor:  0.973
CYP1A2-substrate:  0.921
CYP2C19-inhibitor:  0.464
CYP2C19-substrate:  0.763
CYP2C9-inhibitor:  0.348
CYP2C9-substrate:  0.278
CYP2D6-inhibitor:  0.387
CYP2D6-substrate:  0.134
CYP3A4-inhibitor:  0.039
CYP3A4-substrate:  0.192

ADMET: Excretion

Clearance (CL):  5.803
Half-life (T1/2):  0.757

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.823
Drug-inuced Liver Injury (DILI):  0.306
AMES Toxicity:  0.951
Rat Oral Acute Toxicity:  0.893
Maximum Recommended Daily Dose:  0.745
Skin Sensitization:  0.714
Carcinogencity:  0.88
Eye Corrosion:  0.063
Eye Irritation:  0.919
Respiratory Toxicity:  0.974

Download Data

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

  Natural Product: NPC471751

Natural Product ID:  NPC471751
Common Name*:   (2E)-2-Ethylidene-4-Propan-2-Ylcyclopent-4-Ene-1,3-Dione
IUPAC Name:   (2E)-2-ethylidene-4-propan-2-ylcyclopent-4-ene-1,3-dione
Synonyms:  
Standard InCHIKey:  HDHWQBUJRLQQMJ-QPJJXVBHSA-N
Standard InCHI:  InChI=1S/C10H12O2/c1-4-7-9(11)5-8(6(2)3)10(7)12/h4-6H,1-3H3/b7-4+
SMILES:  C/C=C/1C(=O)C=C(C1=O)C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3113340
PubChem CID:   76310416
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001563] Monocyclic 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
NPO22667 Plectranthus amboinicus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[24491635]
NPO22667 Plectranthus amboinicus Species Lamiaceae 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 23700.0 nM PMID[465031]

☑ 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 NPC471751 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
0.902 High Similarity NPC45283
0.8958 High Similarity NPC471752
0.8654 High Similarity NPC296311
0.8654 High Similarity NPC474141
0.8235 Intermediate Similarity NPC145311
0.82 Intermediate Similarity NPC262558
0.82 Intermediate Similarity NPC8610
0.8163 Intermediate Similarity NPC471753
0.8103 Intermediate Similarity NPC97322
0.8077 Intermediate Similarity NPC58970
0.8077 Intermediate Similarity NPC176819
0.8077 Intermediate Similarity NPC32351
0.8077 Intermediate Similarity NPC163984
0.8 Intermediate Similarity NPC275472
0.8 Intermediate Similarity NPC166788
0.7966 Intermediate Similarity NPC167256
0.7963 Intermediate Similarity NPC268564
0.7857 Intermediate Similarity NPC20603
0.7843 Intermediate Similarity NPC100380
0.78 Intermediate Similarity NPC25771
0.7759 Intermediate Similarity NPC259261
0.7736 Intermediate Similarity NPC228776
0.7719 Intermediate Similarity NPC193695
0.7692 Intermediate Similarity NPC91962
0.7627 Intermediate Similarity NPC25853
0.76 Intermediate Similarity NPC292463
0.7593 Intermediate Similarity NPC64866
0.7593 Intermediate Similarity NPC27438
0.7586 Intermediate Similarity NPC94991
0.7586 Intermediate Similarity NPC266295
0.7586 Intermediate Similarity NPC311852
0.7586 Intermediate Similarity NPC30215
0.7541 Intermediate Similarity NPC212210
0.75 Intermediate Similarity NPC260573
0.75 Intermediate Similarity NPC202850
0.75 Intermediate Similarity NPC4079
0.75 Intermediate Similarity NPC236355
0.75 Intermediate Similarity NPC14917
0.75 Intermediate Similarity NPC475795
0.75 Intermediate Similarity NPC63396
0.7458 Intermediate Similarity NPC143834
0.7458 Intermediate Similarity NPC285594
0.7458 Intermediate Similarity NPC96551
0.7377 Intermediate Similarity NPC165695
0.7377 Intermediate Similarity NPC32285
0.7368 Intermediate Similarity NPC188789
0.7358 Intermediate Similarity NPC324812
0.7308 Intermediate Similarity NPC191337
0.7288 Intermediate Similarity NPC170799
0.7288 Intermediate Similarity NPC308108
0.7258 Intermediate Similarity NPC150162
0.7258 Intermediate Similarity NPC473902
0.7255 Intermediate Similarity NPC301972
0.7241 Intermediate Similarity NPC473733
0.7231 Intermediate Similarity NPC256846
0.7231 Intermediate Similarity NPC67608
0.7213 Intermediate Similarity NPC213152
0.7193 Intermediate Similarity NPC209431
0.7193 Intermediate Similarity NPC100809
0.7188 Intermediate Similarity NPC475523
0.7167 Intermediate Similarity NPC472304
0.7167 Intermediate Similarity NPC276764
0.7143 Intermediate Similarity NPC470329
0.7143 Intermediate Similarity NPC474329
0.7143 Intermediate Similarity NPC251118
0.7143 Intermediate Similarity NPC474304
0.7119 Intermediate Similarity NPC230823
0.7119 Intermediate Similarity NPC55004
0.7119 Intermediate Similarity NPC115385
0.7119 Intermediate Similarity NPC49575
0.7119 Intermediate Similarity NPC267626
0.7115 Intermediate Similarity NPC477686
0.7097 Intermediate Similarity NPC288253
0.7097 Intermediate Similarity NPC322457
0.7091 Intermediate Similarity NPC15325
0.7091 Intermediate Similarity NPC118788
0.7077 Intermediate Similarity NPC469679
0.7077 Intermediate Similarity NPC476614
0.7049 Intermediate Similarity NPC127582
0.7018 Intermediate Similarity NPC23117
0.7018 Intermediate Similarity NPC37644
0.7 Intermediate Similarity NPC27610
0.7 Intermediate Similarity NPC56905
0.7 Intermediate Similarity NPC111474
0.697 Remote Similarity NPC61702
0.697 Remote Similarity NPC162867
0.6939 Remote Similarity NPC130923
0.6935 Remote Similarity NPC60565
0.6923 Remote Similarity NPC216921
0.6875 Remote Similarity NPC38497
0.6866 Remote Similarity NPC2634
0.6866 Remote Similarity NPC265782
0.6866 Remote Similarity NPC251929
0.6852 Remote Similarity NPC22098
0.6852 Remote Similarity NPC276009
0.6852 Remote Similarity NPC195246
0.6833 Remote Similarity NPC192427
0.6833 Remote Similarity NPC192843
0.6833 Remote Similarity NPC281230
0.6825 Remote Similarity NPC190049
0.6818 Remote Similarity NPC469688
0.6818 Remote Similarity NPC260474
0.6818 Remote Similarity NPC155198
0.6818 Remote Similarity NPC87141
0.6818 Remote Similarity NPC188292
0.68 Remote Similarity NPC217923
0.6786 Remote Similarity NPC474391
0.6769 Remote Similarity NPC197089
0.6765 Remote Similarity NPC54123
0.6765 Remote Similarity NPC29328
0.6735 Remote Similarity NPC220061
0.6735 Remote Similarity NPC24833
0.6735 Remote Similarity NPC185839
0.6724 Remote Similarity NPC14002
0.6719 Remote Similarity NPC4638
0.6719 Remote Similarity NPC6697
0.6719 Remote Similarity NPC475124
0.6719 Remote Similarity NPC285371
0.6716 Remote Similarity NPC139397
0.6716 Remote Similarity NPC469914
0.6716 Remote Similarity NPC474060
0.6714 Remote Similarity NPC473171
0.6667 Remote Similarity NPC474228
0.6667 Remote Similarity NPC303613
0.6667 Remote Similarity NPC64985
0.6667 Remote Similarity NPC113082
0.6667 Remote Similarity NPC477458
0.6667 Remote Similarity NPC234829
0.6667 Remote Similarity NPC269641
0.662 Remote Similarity NPC473223
0.6618 Remote Similarity NPC318766
0.6618 Remote Similarity NPC246722
0.6618 Remote Similarity NPC151045
0.6618 Remote Similarity NPC307176
0.6618 Remote Similarity NPC260040
0.6615 Remote Similarity NPC470688
0.6613 Remote Similarity NPC473494
0.661 Remote Similarity NPC95581
0.661 Remote Similarity NPC5626
0.6604 Remote Similarity NPC106819
0.66 Remote Similarity NPC180840
0.66 Remote Similarity NPC155880
0.66 Remote Similarity NPC92863
0.6571 Remote Similarity NPC329866
0.6571 Remote Similarity NPC474796
0.6571 Remote Similarity NPC309852
0.6571 Remote Similarity NPC474797
0.6567 Remote Similarity NPC310992
0.6562 Remote Similarity NPC155849
0.6562 Remote Similarity NPC472306
0.6552 Remote Similarity NPC216407
0.6522 Remote Similarity NPC288667
0.6522 Remote Similarity NPC181204
0.6522 Remote Similarity NPC474562
0.6522 Remote Similarity NPC21944
0.6522 Remote Similarity NPC5701
0.6515 Remote Similarity NPC308294
0.6515 Remote Similarity NPC142423
0.65 Remote Similarity NPC297280
0.6491 Remote Similarity NPC116906
0.6479 Remote Similarity NPC216791
0.6479 Remote Similarity NPC251435
0.6479 Remote Similarity NPC474011
0.6479 Remote Similarity NPC469678
0.6479 Remote Similarity NPC469669
0.6479 Remote Similarity NPC475771
0.6471 Remote Similarity NPC261398
0.6471 Remote Similarity NPC10758
0.6471 Remote Similarity NPC477448
0.6471 Remote Similarity NPC250928
0.6471 Remote Similarity NPC477449
0.6458 Remote Similarity NPC12889
0.6452 Remote Similarity NPC320421
0.6452 Remote Similarity NPC60772
0.6452 Remote Similarity NPC281195
0.6441 Remote Similarity NPC69898
0.6441 Remote Similarity NPC295777
0.6438 Remote Similarity NPC19443
0.6429 Remote Similarity NPC251705
0.6429 Remote Similarity NPC300940
0.6429 Remote Similarity NPC472956
0.6429 Remote Similarity NPC470044
0.6429 Remote Similarity NPC470045
0.6418 Remote Similarity NPC290350
0.6418 Remote Similarity NPC4370
0.6418 Remote Similarity NPC476626
0.6406 Remote Similarity NPC294304
0.6406 Remote Similarity NPC228574
0.6393 Remote Similarity NPC325977
0.6389 Remote Similarity NPC469793
0.6389 Remote Similarity NPC69408
0.6389 Remote Similarity NPC266159
0.6389 Remote Similarity NPC472967
0.6389 Remote Similarity NPC469796
0.6379 Remote Similarity NPC236623
0.6377 Remote Similarity NPC159577
0.6377 Remote Similarity NPC35734
0.6377 Remote Similarity NPC282593
0.6364 Remote Similarity NPC183422
0.6349 Remote Similarity NPC38455

  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 NPC471751 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
0.7288 Intermediate Similarity NPD287 Approved
0.6866 Remote Similarity NPD4691 Approved
0.6716 Remote Similarity NPD4137 Phase 3
0.6618 Remote Similarity NPD4747 Approved
0.6571 Remote Similarity NPD4058 Approved
0.6522 Remote Similarity NPD5276 Approved
0.6515 Remote Similarity NPD7331 Phase 2
0.6471 Remote Similarity NPD5783 Phase 3
0.6338 Remote Similarity NPD5733 Approved
0.6338 Remote Similarity NPD4687 Approved
0.6119 Remote Similarity NPD7341 Phase 2
0.6087 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6066 Remote Similarity NPD539 Approved
0.6061 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6029 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5968 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5844 Remote Similarity NPD4695 Discontinued
0.5823 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5806 Remote Similarity NPD9298 Approved
0.5789 Remote Similarity NPD3174 Discontinued
0.5696 Remote Similarity NPD4223 Phase 3
0.5696 Remote Similarity NPD4221 Approved
0.5696 Remote Similarity NPD5209 Approved
0.561 Remote Similarity NPD5690 Phase 2
0.561 Remote Similarity NPD4519 Discontinued
0.561 Remote Similarity NPD4623 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