Structure

Physi-Chem Properties

Molecular Weight:  248.14
Volume:  272.628
LogP:  1.233
LogD:  1.342
LogS:  -1.979
# Rotatable Bonds:  4
TPSA:  54.37
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.887
Synthetic Accessibility Score:  2.533
Fsp3:  0.467
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.577
MDCK Permeability:  2.575920916569885e-05
Pgp-inhibitor:  0.064
Pgp-substrate:  0.037
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.203
30% Bioavailability (F30%):  0.034

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.814
Plasma Protein Binding (PPB):  74.95953369140625%
Volume Distribution (VD):  0.522
Pgp-substrate:  35.39406967163086%

ADMET: Metabolism

CYP1A2-inhibitor:  0.296
CYP1A2-substrate:  0.918
CYP2C19-inhibitor:  0.332
CYP2C19-substrate:  0.824
CYP2C9-inhibitor:  0.071
CYP2C9-substrate:  0.74
CYP2D6-inhibitor:  0.073
CYP2D6-substrate:  0.894
CYP3A4-inhibitor:  0.031
CYP3A4-substrate:  0.344

ADMET: Excretion

Clearance (CL):  3.589
Half-life (T1/2):  0.506

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.127
Drug-inuced Liver Injury (DILI):  0.199
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.012
Maximum Recommended Daily Dose:  0.441
Skin Sensitization:  0.102
Carcinogencity:  0.058
Eye Corrosion:  0.009
Eye Irritation:  0.49
Respiratory Toxicity:  0.003

Download Data

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

  Natural Product: NPC190049

Natural Product ID:  NPC190049
Common Name*:   Curcumadionol
IUPAC Name:   2-(2-hydroxypropan-2-yl)-6-methyl-5-(3-oxobutyl)cyclohepta-2,4,6-trien-1-one
Synonyms:  
Standard InCHIKey:  ZJOGLHNZNCCGQF-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C15H20O3/c1-10-9-14(17)13(15(3,4)18)8-7-12(10)6-5-11(2)16/h7-9,18H,5-6H2,1-4H3
SMILES:  CC(=O)CCc1ccc(c(=O)cc1C)C(O)(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2386520
PubChem CID:   73356517
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
NPO2618 Curcuma wenyujin Species Zingiberaceae Eukaryota n.a. root n.a. PMID[23738470]
NPO2618 Curcuma wenyujin Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[23738470]
NPO18068 Curcuma phaeocaulis Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[23755850]
NPO2618 Curcuma wenyujin Species Zingiberaceae Eukaryota Rhizomes n.a. n.a. PMID[25275213]
NPO2618 Curcuma wenyujin Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2618 Curcuma wenyujin Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18068 Curcuma phaeocaulis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2618 Curcuma wenyujin Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18068 Curcuma phaeocaulis Species Zingiberaceae 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
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 54200.0 nM PMID[456475]

☑ 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 NPC190049 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
0.9167 High Similarity NPC64985
0.8235 Intermediate Similarity NPC106309
0.8 Intermediate Similarity NPC122244
0.7727 Intermediate Similarity NPC150162
0.7714 Intermediate Similarity NPC288667
0.7606 Intermediate Similarity NPC153660
0.7606 Intermediate Similarity NPC12815
0.7606 Intermediate Similarity NPC215745
0.7606 Intermediate Similarity NPC238948
0.75 Intermediate Similarity NPC308294
0.75 Intermediate Similarity NPC142423
0.7429 Intermediate Similarity NPC136473
0.7419 Intermediate Similarity NPC474127
0.7397 Intermediate Similarity NPC89374
0.7391 Intermediate Similarity NPC278895
0.7333 Intermediate Similarity NPC476627
0.7324 Intermediate Similarity NPC203819
0.7302 Intermediate Similarity NPC297280
0.7297 Intermediate Similarity NPC51391
0.7297 Intermediate Similarity NPC4492
0.726 Intermediate Similarity NPC7382
0.7258 Intermediate Similarity NPC45283
0.7231 Intermediate Similarity NPC281195
0.7188 Intermediate Similarity NPC325977
0.7162 Intermediate Similarity NPC225665
0.7162 Intermediate Similarity NPC166018
0.7162 Intermediate Similarity NPC169056
0.7143 Intermediate Similarity NPC189677
0.7123 Intermediate Similarity NPC275098
0.7105 Intermediate Similarity NPC248624
0.7059 Intermediate Similarity NPC322457
0.7051 Intermediate Similarity NPC275766
0.7013 Intermediate Similarity NPC476624
0.7013 Intermediate Similarity NPC265980
0.7013 Intermediate Similarity NPC472013
0.7013 Intermediate Similarity NPC63326
0.6974 Remote Similarity NPC97173
0.6974 Remote Similarity NPC82666
0.6944 Remote Similarity NPC474060
0.6933 Remote Similarity NPC77501
0.6914 Remote Similarity NPC187529
0.6912 Remote Similarity NPC260573
0.6901 Remote Similarity NPC106613
0.6901 Remote Similarity NPC269985
0.6892 Remote Similarity NPC29542
0.6892 Remote Similarity NPC201562
0.6892 Remote Similarity NPC323437
0.6883 Remote Similarity NPC478122
0.6875 Remote Similarity NPC322461
0.6866 Remote Similarity NPC143834
0.6835 Remote Similarity NPC171665
0.6833 Remote Similarity NPC262558
0.6833 Remote Similarity NPC8610
0.6825 Remote Similarity NPC471751
0.6818 Remote Similarity NPC193695
0.6818 Remote Similarity NPC71755
0.6818 Remote Similarity NPC283502
0.6818 Remote Similarity NPC268185
0.6806 Remote Similarity NPC309466
0.6795 Remote Similarity NPC471890
0.6795 Remote Similarity NPC66677
0.6795 Remote Similarity NPC84185
0.6774 Remote Similarity NPC32351
0.6774 Remote Similarity NPC221467
0.6765 Remote Similarity NPC122521
0.6765 Remote Similarity NPC174447
0.6765 Remote Similarity NPC251042
0.6761 Remote Similarity NPC472072
0.6761 Remote Similarity NPC197089
0.6761 Remote Similarity NPC322035
0.6761 Remote Similarity NPC166791
0.6761 Remote Similarity NPC100719
0.6757 Remote Similarity NPC29328
0.6753 Remote Similarity NPC86917
0.6719 Remote Similarity NPC217188
0.6719 Remote Similarity NPC37644
0.6719 Remote Similarity NPC296311
0.6716 Remote Similarity NPC471619
0.6712 Remote Similarity NPC67608
0.6712 Remote Similarity NPC469914
0.6712 Remote Similarity NPC236208
0.6712 Remote Similarity NPC143396
0.6711 Remote Similarity NPC263698
0.6709 Remote Similarity NPC138492
0.6709 Remote Similarity NPC164218
0.6709 Remote Similarity NPC160582
0.6709 Remote Similarity NPC233352
0.6709 Remote Similarity NPC824
0.6707 Remote Similarity NPC307112
0.6707 Remote Similarity NPC476628
0.6667 Remote Similarity NPC287878
0.6667 Remote Similarity NPC247586
0.6667 Remote Similarity NPC40148
0.6667 Remote Similarity NPC40082
0.6667 Remote Similarity NPC475083
0.6667 Remote Similarity NPC72397
0.6667 Remote Similarity NPC300940
0.6667 Remote Similarity NPC269737
0.6667 Remote Similarity NPC186042
0.6667 Remote Similarity NPC16488
0.6627 Remote Similarity NPC316426
0.6627 Remote Similarity NPC315395
0.6625 Remote Similarity NPC470298
0.6623 Remote Similarity NPC7629
0.6623 Remote Similarity NPC182848
0.6623 Remote Similarity NPC472305
0.6623 Remote Similarity NPC151622
0.6622 Remote Similarity NPC315597
0.6618 Remote Similarity NPC329550
0.6618 Remote Similarity NPC86789
0.6613 Remote Similarity NPC145311
0.6613 Remote Similarity NPC267110
0.6579 Remote Similarity NPC215050
0.6579 Remote Similarity NPC227396
0.6571 Remote Similarity NPC167256
0.6571 Remote Similarity NPC155849
0.6571 Remote Similarity NPC477830
0.6562 Remote Similarity NPC46565
0.6562 Remote Similarity NPC229046
0.6548 Remote Similarity NPC113370
0.6548 Remote Similarity NPC476079
0.6548 Remote Similarity NPC103743
0.6548 Remote Similarity NPC23622
0.6543 Remote Similarity NPC133844
0.6543 Remote Similarity NPC85772
0.6543 Remote Similarity NPC20262
0.6543 Remote Similarity NPC227925
0.6543 Remote Similarity NPC256750
0.6538 Remote Similarity NPC34110
0.6538 Remote Similarity NPC473536
0.6538 Remote Similarity NPC316324
0.6538 Remote Similarity NPC472014
0.6538 Remote Similarity NPC180290
0.6538 Remote Similarity NPC471061
0.6533 Remote Similarity NPC319163
0.6533 Remote Similarity NPC21944
0.6533 Remote Similarity NPC67076
0.6533 Remote Similarity NPC474884
0.6533 Remote Similarity NPC95863
0.6533 Remote Similarity NPC126061
0.6533 Remote Similarity NPC84790
0.6528 Remote Similarity NPC137163
0.6515 Remote Similarity NPC188789
0.6515 Remote Similarity NPC275472
0.6512 Remote Similarity NPC77337
0.6508 Remote Similarity NPC225974
0.6508 Remote Similarity NPC288381
0.6508 Remote Similarity NPC20934
0.6508 Remote Similarity NPC228776
0.6508 Remote Similarity NPC58970
0.6508 Remote Similarity NPC176819
0.6508 Remote Similarity NPC163984
0.6506 Remote Similarity NPC15807
0.6506 Remote Similarity NPC261380
0.65 Remote Similarity NPC25771
0.65 Remote Similarity NPC45495
0.6494 Remote Similarity NPC260396
0.6486 Remote Similarity NPC473277
0.6471 Remote Similarity NPC320421
0.6471 Remote Similarity NPC311852
0.6471 Remote Similarity NPC58532
0.6471 Remote Similarity NPC472677
0.6471 Remote Similarity NPC34416
0.6463 Remote Similarity NPC477784
0.6463 Remote Similarity NPC477786
0.6463 Remote Similarity NPC477785
0.6462 Remote Similarity NPC268564
0.6462 Remote Similarity NPC474141
0.6462 Remote Similarity NPC61177
0.6456 Remote Similarity NPC207772
0.6456 Remote Similarity NPC315765
0.6456 Remote Similarity NPC169095
0.6456 Remote Similarity NPC231739
0.6456 Remote Similarity NPC475994
0.6441 Remote Similarity NPC209279
0.6441 Remote Similarity NPC180871
0.6441 Remote Similarity NPC67761
0.6441 Remote Similarity NPC51758
0.6441 Remote Similarity NPC194586
0.6441 Remote Similarity NPC108494
0.6441 Remote Similarity NPC68889
0.6441 Remote Similarity NPC88079
0.6438 Remote Similarity NPC21998
0.6438 Remote Similarity NPC254886
0.6437 Remote Similarity NPC142838
0.6429 Remote Similarity NPC263732
0.6418 Remote Similarity NPC324224
0.6418 Remote Similarity NPC472808
0.641 Remote Similarity NPC205615
0.641 Remote Similarity NPC256640
0.641 Remote Similarity NPC474197
0.641 Remote Similarity NPC110725
0.641 Remote Similarity NPC16279
0.641 Remote Similarity NPC215481
0.6406 Remote Similarity NPC64866
0.6406 Remote Similarity NPC43053
0.6406 Remote Similarity NPC477458
0.64 Remote Similarity NPC67183
0.64 Remote Similarity NPC315285
0.64 Remote Similarity NPC286154

  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 NPC190049 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
0.6761 Remote Similarity NPD7331 Phase 2
0.6538 Remote Similarity NPD4756 Discovery
0.6349 Remote Similarity NPD4220 Pre-registration
0.6338 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6286 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6197 Remote Similarity NPD4191 Approved
0.6197 Remote Similarity NPD4192 Approved
0.6197 Remote Similarity NPD4193 Approved
0.6197 Remote Similarity NPD4194 Approved
0.6164 Remote Similarity NPD7341 Phase 2
0.6118 Remote Similarity NPD1696 Phase 3
0.6118 Remote Similarity NPD5363 Approved
0.5952 Remote Similarity NPD5209 Approved
0.5904 Remote Similarity NPD4252 Approved
0.5904 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5882 Remote Similarity NPD539 Approved
0.5862 Remote Similarity NPD4623 Approved
0.5862 Remote Similarity NPD4519 Discontinued
0.5846 Remote Similarity NPD3173 Approved
0.5806 Remote Similarity NPD9411 Phase 1
0.5797 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5789 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5778 Remote Similarity NPD5785 Approved
0.5775 Remote Similarity NPD287 Approved
0.5765 Remote Similarity NPD4269 Approved
0.5765 Remote Similarity NPD4270 Approved
0.5765 Remote Similarity NPD4800 Clinical (unspecified phase)
0.5753 Remote Similarity NPD368 Approved
0.575 Remote Similarity NPD4058 Approved
0.5735 Remote Similarity NPD3172 Approved
0.5714 Remote Similarity NPD4695 Discontinued
0.5696 Remote Similarity NPD5276 Approved
0.5682 Remote Similarity NPD4694 Approved
0.5682 Remote Similarity NPD5280 Approved
0.5682 Remote Similarity NPD3574 Clinical (unspecified phase)
0.5667 Remote Similarity NPD5783 Phase 3
0.5663 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5658 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5652 Remote Similarity NPD3194 Approved
0.5652 Remote Similarity NPD4266 Approved
0.5652 Remote Similarity NPD3195 Phase 2
0.5652 Remote Similarity NPD3196 Approved
0.5625 Remote Similarity NPD39 Approved
0.5625 Remote Similarity NPD4265 Approved
0.5625 Remote Similarity NPD4222 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