Structure

Physi-Chem Properties

Molecular Weight:  172.15
Volume:  190.54
LogP:  1.878
LogD:  2.026
LogS:  -0.999
# Rotatable Bonds:  1
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.63
Synthetic Accessibility Score:  3.6
Fsp3:  1.0
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:  -4.416
MDCK Permeability:  1.9898812752217054e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.88
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.831
Plasma Protein Binding (PPB):  73.9889907836914%
Volume Distribution (VD):  0.951
Pgp-substrate:  31.31587791442871%

ADMET: Metabolism

CYP1A2-inhibitor:  0.066
CYP1A2-substrate:  0.491
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.83
CYP2C9-inhibitor:  0.047
CYP2C9-substrate:  0.883
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.205
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.138

ADMET: Excretion

Clearance (CL):  7.414
Half-life (T1/2):  0.682

ADMET: Toxicity

hERG Blockers:  0.03
Human Hepatotoxicity (H-HT):  0.054
Drug-inuced Liver Injury (DILI):  0.18
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.023
Maximum Recommended Daily Dose:  0.036
Skin Sensitization:  0.548
Carcinogencity:  0.049
Eye Corrosion:  0.974
Eye Irritation:  0.991
Respiratory Toxicity:  0.04

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

  Natural Product: NPC54145

Natural Product ID:  NPC54145
Common Name*:   LMXFTMYMHGYJEI-IWSPIJDZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LMXFTMYMHGYJEI-IWSPIJDZSA-N
Standard InCHI:  InChI=1S/C10H20O2/c1-7-4-5-8(9(11)6-7)10(2,3)12/h7-9,11-12H,4-6H2,1-3H3/t7-,8-,9-/m1/s1
SMILES:  C[C@@H]1CC[C@H]([C@@H](C1)O)C(C)(C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   19100
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001401] Menthane 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
NPO24176 Streptomyces fradiae Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[10757717]
NPO23281 Aplysinella rhax Species Aplysinellidae Eukaryota n.a. n.a. n.a. PMID[10757728]
NPO24219 Erylus nobilis Species n.a. n.a. n.a. n.a. n.a. PMID[11421740]
NPO24219 Erylus nobilis Species n.a. n.a. n.a. n.a. n.a. PMID[11908993]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[11914965]
NPO24364 Petrosia corticata Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[12350165]
NPO27883 Bursera simaruba Species Burseraceae Eukaryota Resin n.a. n.a. PMID[1294696]
NPO24364 Petrosia corticata Species Petrosiidae Eukaryota n.a. Okinawan, Japan n.a. PMID[14695804]
NPO28935 Ericameria laricifolia Species Asteraceae Eukaryota n.a. Sonoran Desert n.a. PMID[15043404]
NPO24364 Petrosia corticata Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[15332859]
NPO15538 Eucalyptus citriodora Species Myrtaceae Eukaryota Leaves the campus of Panjab University, Chandigarh, India PMID[16989303]
NPO24364 Petrosia corticata Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[17407351]
NPO23281 Aplysinella rhax Species Aplysinellidae Eukaryota n.a. n.a. n.a. PMID[17827010]
NPO20637 Piper acutifolium Species Piperaceae Eukaryota n.a. leaf n.a. PMID[18712933]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. aerial part n.a. PMID[18991207]
NPO27883 Bursera simaruba Species Burseraceae Eukaryota n.a. bark n.a. PMID[19329133]
NPO23924 Psilotum nudum Species Psilotaceae Eukaryota n.a. n.a. n.a. PMID[20488581]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota essential oil Tibet n.a. PMID[20944522]
NPO23499 Carpesium faberi Species Asteraceae Eukaryota whole plant Changshou County, Chongqing, China 2008-Aug PMID[21109433]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota Roots n.a. n.a. PMID[24054487]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota roots n.a. n.a. PMID[24412339]
NPO15538 Eucalyptus citriodora Species Myrtaceae Eukaryota Essential oil n.a. n.a. PMID[24641242]
NPO24364 Petrosia corticata Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[25987373]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[27116034]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota Twigs n.a. n.a. PMID[28541690]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[29667821]
NPO24364 Petrosia corticata Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[7807132]
NPO27903 Delphinium denudatum Species Ranunculaceae Eukaryota n.a. root n.a. PMID[9170290]
NPO22455 Corydalis sewerzowi Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21625 Bidens tripartita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23924 Psilotum nudum Species Psilotaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26851 Eupatorium rebaudianum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27903 Delphinium denudatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27903 Delphinium denudatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22455 Corydalis sewerzowi Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18780 Diplacus aurantiacus Species Phrymaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15538 Eucalyptus citriodora Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1079 Vachellia karroo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26851 Eupatorium rebaudianum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21625 Bidens tripartita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23924 Psilotum nudum Species Psilotaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24090 Aplysilla rosea Species Darwinellidae Eukaryota n.a. Austrila n.a. Database[Title]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26549 Polanisia trachysperma Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29110 Litsea cubeba Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19535 Senecio zoellneri Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22455 Corydalis sewerzowi Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27903 Delphinium denudatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24219 Erylus nobilis Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO28959 Cissus quadrangularis Species Vitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20637 Piper acutifolium Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23318 Aconitum palmatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13127 Vallaris heynei Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29377 Callistemon speciosus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16079 Cephalaria leucantha Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27256 Solanum boerhaavii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8593 Zygosaccharomyces rouxii Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23920 Amanita pseudoporphyria Species Amanitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15538 Eucalyptus citriodora Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18976 Centaurea arbutifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23792 Gomphostemma parviflorum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23364 Lambertella corni Species Rutstroemiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12429 Acicarpha tribuloides Species Calyceraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24290 Claviceps microcephala Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO862 Podocarpus elatus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23459 Onoseris alata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29218 Ramalina farinacea Species Ramalinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24249 Codonopsis cordifolioidea Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23211 Xyris indica Species Xyridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24408 Ariocarpus fissuratus Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24364 Petrosia corticata Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23545 Vellozia streptophylla Species Velloziaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24445 Arbacia pustulosa Species Arbaciidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21827 Albatrellus caeruleoporus Species Albatrellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23961 Scytonema ocellatum Species Scytonemataceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO23834 Chlamydomonas allensworthii Species Chlamydomonadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23043 Cryptolestes pusillus Species Laemophloeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22143 Genista sessilifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23413 Crematogaster africana Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21625 Bidens tripartita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24005 Mytilus galloprovincialis Species Mytilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22324 Erium villosum Species Pseudococcidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24176 Streptomyces fradiae Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO29411 Streptomyces nigrescens Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO27562 Coleus wulfenioides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20998 Machaerium kuhlmannii Species Dolichopodidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23499 Carpesium faberi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5782 Aniba rosaeodora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24132 Euphausia superba Species Euphausiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27883 Bursera simaruba Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23924 Psilotum nudum Species Psilotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO738 Dahlstedtia pentaphylla Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22595 Trapa bicornis Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24048 Cladonia pityrea Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29144 Ormosia fordiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23281 Aplysinella rhax Species Aplysinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28549 Mentha incana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1079 Vachellia karroo Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29307 Loranthus longiflorus Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16043 Centaurea musimomum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23739 Staehelina fruticosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24090 Aplysilla rosea Species Darwinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26851 Eupatorium rebaudianum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17737 Lepidorhinus squamosus n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO23114 Cacalia robusta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23696 Solanum diflorum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23884 Hippobroma longiflora Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27724 Polygala senega Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28935 Ericameria laricifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18780 Diplacus aurantiacus Species Phrymaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23610 Aconitum tianschanicum Species Ranunculaceae 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

☑ 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 NPC54145 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

  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 NPC54145 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

  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