Structure

Physi-Chem Properties

Molecular Weight:  164.08
Volume:  179.994
LogP:  1.614
LogD:  1.347
LogS:  -1.714
# Rotatable Bonds:  1
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.688
Synthetic Accessibility Score:  1.988
Fsp3:  0.3
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.382
MDCK Permeability:  2.975711686303839e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.018
30% Bioavailability (F30%):  0.148

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.633
Plasma Protein Binding (PPB):  89.74959564208984%
Volume Distribution (VD):  0.574
Pgp-substrate:  10.968795776367188%

ADMET: Metabolism

CYP1A2-inhibitor:  0.861
CYP1A2-substrate:  0.93
CYP2C19-inhibitor:  0.356
CYP2C19-substrate:  0.792
CYP2C9-inhibitor:  0.292
CYP2C9-substrate:  0.719
CYP2D6-inhibitor:  0.083
CYP2D6-substrate:  0.401
CYP3A4-inhibitor:  0.041
CYP3A4-substrate:  0.362

ADMET: Excretion

Clearance (CL):  2.882
Half-life (T1/2):  0.746

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.025
Drug-inuced Liver Injury (DILI):  0.354
AMES Toxicity:  0.217
Rat Oral Acute Toxicity:  0.56
Maximum Recommended Daily Dose:  0.037
Skin Sensitization:  0.601
Carcinogencity:  0.424
Eye Corrosion:  0.03
Eye Irritation:  0.947
Respiratory Toxicity:  0.695

Download Data

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

  Natural Product: NPC281195

Natural Product ID:  NPC281195
Common Name*:   Alpha-Thujaplicin
IUPAC Name:   2-hydroxy-3-propan-2-ylcyclohepta-2,4,6-trien-1-one
Synonyms:  
Standard InCHIKey:  TUFYVOCKVJOUIR-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H12O2/c1-7(2)8-5-3-4-6-9(11)10(8)12/h3-7H,1-2H3,(H,11,12)
SMILES:  CC(c1ccccc(c1=O)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1275969
PubChem CID:   80297
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004150] Hydrocarbon derivatives
      • [CHEMONTID:0001650] Tropones
        • [CHEMONTID:0001674] Tropolones

*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
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Leaves n.a. n.a. PMID[12088434]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21707257]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO28445 Juniperus taiwaniana Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28445 Juniperus taiwaniana Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19472 Thymus vulgaris 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
NPT43 Individual Protein Tyrosinase Agaricus bisporus IC50 = 9530.0 nM PMID[545511]
NPT43 Individual Protein Tyrosinase Agaricus bisporus Ki = 3300.0 nM PMID[545511]
NPT43 Individual Protein Tyrosinase Agaricus bisporus Km = 380000.0 nM PMID[545511]
NPT168 Cell Line P388 Mus musculus GI = 100.0 % PMID[545512]
NPT168 Cell Line P388 Mus musculus GI = 68.0 % PMID[545512]
NPT168 Cell Line P388 Mus musculus GI = 98.0 % PMID[545512]
NPT168 Cell Line P388 Mus musculus GI = 78.0 % PMID[545512]
NPT43 Individual Protein Tyrosinase Agaricus bisporus IC50 = 9530.0 nM PMID[545513]
NPT43 Individual Protein Tyrosinase Agaricus bisporus IC50 = 9530.0 nM PMID[545515]
NPT32 Organism Mus musculus Mus musculus LD50 = 256.0 mg.kg-1 PMID[545512]
NPT2525 Organism Dermatophagoides farinae Dermatophagoides farinae LC50 = 0.66 g/m2 PMID[545512]
NPT847 Organism Reticulitermes speratus Reticulitermes speratus LC50 = 0.02 g/m2 PMID[545512]
NPT2525 Organism Dermatophagoides farinae Dermatophagoides farinae mortality = 1.1 % PMID[545512]
NPT2525 Organism Dermatophagoides farinae Dermatophagoides farinae mortality = 0.0 % PMID[545512]
NPT2525 Organism Dermatophagoides farinae Dermatophagoides farinae mortality = 38.4 % PMID[545512]
NPT2525 Organism Dermatophagoides farinae Dermatophagoides farinae mortality = 69.5 % PMID[545512]
NPT847 Organism Reticulitermes speratus Reticulitermes speratus mortality = 0.0 % PMID[545512]
NPT847 Organism Reticulitermes speratus Reticulitermes speratus mortality = 100.0 % PMID[545512]
NPT847 Organism Reticulitermes speratus Reticulitermes speratus mortality = 13.3 % PMID[545512]
NPT847 Organism Reticulitermes speratus Reticulitermes speratus mortality = 93.3 % PMID[545512]
NPT1465 Organism Legionella pneumophila Legionella pneumophila MIC = 50.0 ug.mL-1 PMID[545512]
NPT1465 Organism Legionella pneumophila Legionella pneumophila MIC = 12.5 ug.mL-1 PMID[545512]
NPT2637 Organism Colletotrichum lagenarium Colletotrichum lagenarium MIC = 12.0 ug.mL-1 PMID[545512]
NPT2975 Organism Colletotrichum orbiculare Colletotrichum orbiculare MIC = 12.0 ug.mL-1 PMID[545512]
NPT852 Organism Phomopsis obscurans Phomopsis obscurans MIC = 12.0 ug.mL-1 PMID[545512]
NPT635 Organism Botryotinia fuckeliana Botryotinia fuckeliana MIC = 25.0 ug.mL-1 PMID[545512]
NPT2600 Organism Fusarium solani Fusarium solani MIC = 50.0 ug.mL-1 PMID[545512]
NPT2976 Organism Thanatephorus cucumeris Thanatephorus cucumeris MIC = 12.0 ug.mL-1 PMID[545512]
NPT961 Organism Pythium aphanidermatum Pythium aphanidermatum MIC = 12.0 ug.mL-1 PMID[545512]
NPT2 Others Unspecified Ratio IC50 > 104.93 n.a. PMID[545513]
NPT741 Individual Protein Tyrosinase Homo sapiens Ratio IC50 < 0.57 n.a. PMID[545513]
NPT741 Individual Protein Tyrosinase Homo sapiens IC50 > 1000000.0 nM PMID[545513]
NPT2 Others Unspecified IC50 = 50000.0 nM PMID[545514]
NPT2 Others Unspecified IC50 = 33000.0 nM PMID[545514]
NPT2 Others Unspecified IC50 > 100000.0 nM PMID[545514]
NPT2 Others Unspecified IC50 = 12000.0 nM PMID[545514]
NPT2 Others Unspecified Ratio IC50 > 105.0 n.a. PMID[545515]

☑ 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 NPC281195 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
0.8889 High Similarity NPC229046
0.8889 High Similarity NPC46565
0.875 High Similarity NPC297280
0.7895 Intermediate Similarity NPC137396
0.75 Intermediate Similarity NPC322457
0.7353 Intermediate Similarity NPC474060
0.7231 Intermediate Similarity NPC190049
0.7167 Intermediate Similarity NPC474805
0.7143 Intermediate Similarity NPC320421
0.7143 Intermediate Similarity NPC166788
0.7143 Intermediate Similarity NPC288667
0.7049 Intermediate Similarity NPC322461
0.7031 Intermediate Similarity NPC38455
0.6986 Remote Similarity NPC110725
0.697 Remote Similarity NPC477830
0.6944 Remote Similarity NPC122244
0.6901 Remote Similarity NPC106309
0.6866 Remote Similarity NPC475618
0.6825 Remote Similarity NPC325977
0.6818 Remote Similarity NPC64985
0.678 Remote Similarity NPC313553
0.6774 Remote Similarity NPC317796
0.6774 Remote Similarity NPC474127
0.6774 Remote Similarity NPC300121
0.6774 Remote Similarity NPC129710
0.6724 Remote Similarity NPC262558
0.6724 Remote Similarity NPC8610
0.6719 Remote Similarity NPC71755
0.6719 Remote Similarity NPC192843
0.6719 Remote Similarity NPC281230
0.6716 Remote Similarity NPC53109
0.6716 Remote Similarity NPC143168
0.6712 Remote Similarity NPC147438
0.6711 Remote Similarity NPC27817
0.6667 Remote Similarity NPC118788
0.6667 Remote Similarity NPC225974
0.6667 Remote Similarity NPC197089
0.6667 Remote Similarity NPC471753
0.6667 Remote Similarity NPC220191
0.6625 Remote Similarity NPC470177
0.662 Remote Similarity NPC262673
0.6618 Remote Similarity NPC7029
0.6618 Remote Similarity NPC150162
0.6613 Remote Similarity NPC45283
0.6613 Remote Similarity NPC37644
0.6579 Remote Similarity NPC248624
0.6575 Remote Similarity NPC215745
0.6575 Remote Similarity NPC238948
0.6575 Remote Similarity NPC12815
0.6567 Remote Similarity NPC269737
0.6557 Remote Similarity NPC48162
0.6557 Remote Similarity NPC22329
0.6538 Remote Similarity NPC225515
0.6533 Remote Similarity NPC26504
0.6528 Remote Similarity NPC203819
0.6528 Remote Similarity NPC94743
0.6528 Remote Similarity NPC318766
0.6528 Remote Similarity NPC291062
0.6522 Remote Similarity NPC471566
0.6515 Remote Similarity NPC329550
0.6515 Remote Similarity NPC473494
0.6491 Remote Similarity NPC216921
0.6479 Remote Similarity NPC309466
0.6462 Remote Similarity NPC200831
0.6462 Remote Similarity NPC299369
0.6462 Remote Similarity NPC268185
0.6462 Remote Similarity NPC224103
0.6452 Remote Similarity NPC471751
0.6447 Remote Similarity NPC82666
0.6447 Remote Similarity NPC97173
0.6441 Remote Similarity NPC471752
0.6438 Remote Similarity NPC474884
0.6429 Remote Similarity NPC308294
0.6429 Remote Similarity NPC142423
0.6418 Remote Similarity NPC122521
0.6418 Remote Similarity NPC174447
0.6418 Remote Similarity NPC251042
0.6393 Remote Similarity NPC176819
0.6393 Remote Similarity NPC221467
0.6393 Remote Similarity NPC163984
0.6393 Remote Similarity NPC58970
0.6389 Remote Similarity NPC10758
0.6389 Remote Similarity NPC250928
0.6379 Remote Similarity NPC477686
0.6364 Remote Similarity NPC471619
0.6364 Remote Similarity NPC139056
0.6351 Remote Similarity NPC153660
0.6338 Remote Similarity NPC243272
0.6338 Remote Similarity NPC106613
0.6338 Remote Similarity NPC251429
0.6329 Remote Similarity NPC275766
0.6324 Remote Similarity NPC40082
0.6324 Remote Similarity NPC260573
0.6316 Remote Similarity NPC1254
0.6316 Remote Similarity NPC51391
0.6316 Remote Similarity NPC4492
0.6301 Remote Similarity NPC107848
0.6301 Remote Similarity NPC286154
0.6286 Remote Similarity NPC471565
0.6271 Remote Similarity NPC191337
0.6269 Remote Similarity NPC203233
0.6269 Remote Similarity NPC143834
0.6267 Remote Similarity NPC264178
0.625 Remote Similarity NPC263382
0.625 Remote Similarity NPC111474
0.625 Remote Similarity NPC125578
0.625 Remote Similarity NPC146376
0.625 Remote Similarity NPC476614
0.6234 Remote Similarity NPC476007
0.6234 Remote Similarity NPC211279
0.6232 Remote Similarity NPC477707
0.6232 Remote Similarity NPC57463
0.6232 Remote Similarity NPC151728
0.622 Remote Similarity NPC32037
0.6216 Remote Similarity NPC316185
0.6216 Remote Similarity NPC474539
0.6216 Remote Similarity NPC95863
0.6212 Remote Similarity NPC193695
0.6212 Remote Similarity NPC474825
0.6203 Remote Similarity NPC108955
0.6203 Remote Similarity NPC74086
0.6197 Remote Similarity NPC16119
0.6197 Remote Similarity NPC315115
0.6197 Remote Similarity NPC137163
0.619 Remote Similarity NPC60765
0.6184 Remote Similarity NPC474885
0.6184 Remote Similarity NPC263698
0.6184 Remote Similarity NPC315552
0.6164 Remote Similarity NPC94488
0.6164 Remote Similarity NPC473603
0.6164 Remote Similarity NPC476059
0.6164 Remote Similarity NPC469914
0.6164 Remote Similarity NPC136473
0.6163 Remote Similarity NPC45579
0.6154 Remote Similarity NPC189485
0.6154 Remote Similarity NPC99182
0.6154 Remote Similarity NPC67367
0.6143 Remote Similarity NPC474400
0.6143 Remote Similarity NPC34622
0.6133 Remote Similarity NPC316851
0.6133 Remote Similarity NPC300940
0.6129 Remote Similarity NPC32351
0.6129 Remote Similarity NPC20934
0.6129 Remote Similarity NPC228776
0.6129 Remote Similarity NPC15325
0.6129 Remote Similarity NPC288381
0.6125 Remote Similarity NPC55869
0.6119 Remote Similarity NPC311852
0.6118 Remote Similarity NPC210216
0.6111 Remote Similarity NPC474619
0.6111 Remote Similarity NPC278895
0.6111 Remote Similarity NPC38497
0.6104 Remote Similarity NPC472967
0.6104 Remote Similarity NPC250621
0.6104 Remote Similarity NPC266159
0.6098 Remote Similarity NPC469884
0.6094 Remote Similarity NPC284224
0.6094 Remote Similarity NPC296311
0.6094 Remote Similarity NPC217188
0.6081 Remote Similarity NPC59558
0.6076 Remote Similarity NPC472965
0.6076 Remote Similarity NPC63326
0.6076 Remote Similarity NPC63649
0.6076 Remote Similarity NPC265980
0.6076 Remote Similarity NPC264227
0.6061 Remote Similarity NPC324224
0.6061 Remote Similarity NPC472808
0.6056 Remote Similarity NPC471556
0.6056 Remote Similarity NPC101670
0.6056 Remote Similarity NPC470688
0.6056 Remote Similarity NPC474304
0.6056 Remote Similarity NPC98897
0.6056 Remote Similarity NPC474329
0.6053 Remote Similarity NPC315843
0.6053 Remote Similarity NPC107654
0.6034 Remote Similarity NPC209279
0.6034 Remote Similarity NPC51758
0.6034 Remote Similarity NPC194586
0.6034 Remote Similarity NPC67761
0.6034 Remote Similarity NPC68889
0.6034 Remote Similarity NPC88079
0.6034 Remote Similarity NPC108494
0.6034 Remote Similarity NPC180871
0.6032 Remote Similarity NPC477458
0.6032 Remote Similarity NPC43053
0.6029 Remote Similarity NPC106851
0.6029 Remote Similarity NPC133600
0.6029 Remote Similarity NPC278202
0.6029 Remote Similarity NPC274927
0.6027 Remote Similarity NPC287705
0.6027 Remote Similarity NPC313444
0.6027 Remote Similarity NPC117804
0.6026 Remote Similarity NPC180290
0.6 Remote Similarity NPC319163
0.6 Remote Similarity NPC474202
0.6 Remote Similarity NPC117572
0.6 Remote Similarity NPC155849
0.6 Remote Similarity NPC185839
0.6 Remote Similarity NPC189677
0.6 Remote Similarity NPC158853

  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 NPC281195 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
0.6774 Remote Similarity NPD539 Approved
0.6716 Remote Similarity NPD2664 Clinical (unspecified phase)
0.6462 Remote Similarity NPD8779 Phase 3
0.6234 Remote Similarity NPD4756 Discovery
0.6203 Remote Similarity NPD4695 Discontinued
0.6203 Remote Similarity NPD8259 Clinical (unspecified phase)
0.6197 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6061 Remote Similarity NPD9286 Clinical (unspecified phase)
0.6 Remote Similarity NPD4222 Approved
0.6 Remote Similarity NPD9090 Phase 3
0.5972 Remote Similarity NPD7331 Phase 2
0.5968 Remote Similarity NPD4220 Pre-registration
0.5789 Remote Similarity NPD5783 Phase 3
0.5753 Remote Similarity NPD3704 Approved
0.5738 Remote Similarity NPD39 Approved
0.5735 Remote Similarity NPD9287 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3173 Approved
0.5667 Remote Similarity NPD5326 Phase 3
0.5652 Remote Similarity NPD6109 Phase 1
0.5647 Remote Similarity NPD1696 Phase 3
0.5616 Remote Similarity NPD7341 Phase 2

  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