Structure

Physi-Chem Properties

Molecular Weight:  290.26
Volume:  340.881
LogP:  6.058
LogD:  4.338
LogS:  -5.027
# Rotatable Bonds:  4
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.677
Synthetic Accessibility Score:  3.959
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.463
MDCK Permeability:  1.1433441613917239e-05
Pgp-inhibitor:  0.805
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.991
30% Bioavailability (F30%):  0.752

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.47
Plasma Protein Binding (PPB):  90.6911849975586%
Volume Distribution (VD):  1.265
Pgp-substrate:  5.591266632080078%

ADMET: Metabolism

CYP1A2-inhibitor:  0.233
CYP1A2-substrate:  0.15
CYP2C19-inhibitor:  0.137
CYP2C19-substrate:  0.648
CYP2C9-inhibitor:  0.307
CYP2C9-substrate:  0.349
CYP2D6-inhibitor:  0.019
CYP2D6-substrate:  0.424
CYP3A4-inhibitor:  0.296
CYP3A4-substrate:  0.231

ADMET: Excretion

Clearance (CL):  11.86
Half-life (T1/2):  0.083

ADMET: Toxicity

hERG Blockers:  0.043
Human Hepatotoxicity (H-HT):  0.6
Drug-inuced Liver Injury (DILI):  0.046
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.503
Maximum Recommended Daily Dose:  0.579
Skin Sensitization:  0.585
Carcinogencity:  0.877
Eye Corrosion:  0.28
Eye Irritation:  0.511
Respiratory Toxicity:  0.954

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  Natural Product: NPC118426

Natural Product ID:  NPC118426
Common Name*:   NERNKRPBSOBEHC-CMKODMSKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NERNKRPBSOBEHC-CMKODMSKSA-N
Standard InCHI:  InChI=1S/C20H34O/c1-15(11-14-21)7-9-17-16(2)8-10-18-19(3,4)12-6-13-20(17,18)5/h11,17-18,21H,2,6-10,12-14H2,1,3-5H3/t17-,18-,20+/m0/s1
SMILES:  CC(=CCO)CC[C@H]1C(=C)CC[C@H]2C(C)(C)CCC[C@]12C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   131860474
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids

*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
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jep.2005.01.054]
NPO27604 Erythrina burttii Species Fabaceae Eukaryota n.a. root n.a. DOI[10.1016/S0031-9422(01)00459-9]
NPO27847 Suillus granulatus Species Suillaceae Eukaryota n.a. n.a. n.a. PMID[11575963]
NPO27604 Erythrina burttii Species Fabaceae Eukaryota n.a. stem n.a. PMID[12770595]
NPO27847 Suillus granulatus Species Suillaceae Eukaryota n.a. n.a. n.a. PMID[1294697]
NPO27878 Viola hondoensis Species Violaceae Eukaryota n.a. whole plant n.a. PMID[15356999]
NPO28378 Kokoona ochracea Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[1800637]
NPO20443 Cratoxylum pruniflorum Species Hypericaceae Eukaryota roots n.a. n.a. PMID[24940955]
NPO27847 Suillus granulatus Species Suillaceae Eukaryota n.a. n.a. n.a. PMID[2607355]
NPO27847 Suillus granulatus Species Suillaceae Eukaryota n.a. n.a. n.a. PMID[2809609]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Seeds n.a. n.a. PMID[28134521]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31181920]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31418264]
NPO28378 Kokoona ochracea Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[8158155]
NPO28378 Kokoona ochracea Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[8277307]
NPO20443 Cratoxylum pruniflorum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Stem Bark n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28124 Tamarix gallica Species Tamaricaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27689 Mentha pulegium Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28378 Kokoona ochracea Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27604 Erythrina burttii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28378 Kokoona ochracea Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28433 Russula queletii Species Russulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14888 Pelargonium x hortorum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28124 Tamarix gallica Species Tamaricaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27604 Erythrina burttii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27689 Mentha pulegium Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28191 Hardwickia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28139 Umbilicaria pustulata Species Umbilicariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28174 Poterium sanguisorba Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14888 Pelargonium x hortorum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27480 Pinna muricata Species Pinnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28262 Marasmius graminum Species Marasmiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4094 Aspergillus ruber Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28253 Ceratiomyxa fruticulosa Species Ceratiomyxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28555 Adina trichotoma Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28499 Aethalium septicum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO28049 Piper callosum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27878 Viola hondoensis Species Violaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20121 Afraegle paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28074 Dianella revoluta Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28512 Astragalus glycyphyllos Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28305 Daphnandra johnsonii Species Atherospermataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17152 Pittocaulon bombycophole Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28061 Gyrothyra underwoodiana Species Gyrothyraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27220 Centaurea cheiranthifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27532 Lamprolobium fruticosum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27318 Sideritis lanata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27681 Mikania grazielae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28330 Colchicum arenarium Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28378 Kokoona ochracea Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20443 Cratoxylum pruniflorum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23272 Cassinia subtropica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16927 Erodendrum neriifolium n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO28433 Russula queletii Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28124 Tamarix gallica Species Tamaricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28321 Cortinellus berkeleyanus n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO28568 Hippeastrum aulicum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27894 Rubus pungens Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16983 Persea obovatifolia Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28168 Armina maculata Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28534 Athrixia elata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4266 Botryotrichum murorum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27350 Scytalidium uredinicola Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27334 Siphula roccellaeformis Species Icmadophilaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27689 Mentha pulegium Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27604 Erythrina burttii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28006 Pinus pumila Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27847 Suillus granulatus Species Suillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9367 Jacobaea argunensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15295 Polyachyrus sphaerocephalus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28345 Cladanthus arabicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28208 Salvia dichroa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27861 Laggera aurita Species Asteraceae 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 NPC118426 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 NPC118426 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