Structure

Physi-Chem Properties

Molecular Weight:  598.28
Volume:  603.352
LogP:  4.184
LogD:  2.663
LogS:  -4.89
# Rotatable Bonds:  10
TPSA:  130.87
# H-Bond Aceptor:  10
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.189
Synthetic Accessibility Score:  5.902
Fsp3:  0.636
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.277
MDCK Permeability:  7.330969674512744e-05
Pgp-inhibitor:  1.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.074
20% Bioavailability (F20%):  0.853
30% Bioavailability (F30%):  0.325

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.023
Plasma Protein Binding (PPB):  80.12738800048828%
Volume Distribution (VD):  2.098
Pgp-substrate:  15.689044952392578%

ADMET: Metabolism

CYP1A2-inhibitor:  0.021
CYP1A2-substrate:  0.061
CYP2C19-inhibitor:  0.523
CYP2C19-substrate:  0.437
CYP2C9-inhibitor:  0.901
CYP2C9-substrate:  0.01
CYP2D6-inhibitor:  0.138
CYP2D6-substrate:  0.052
CYP3A4-inhibitor:  0.916
CYP3A4-substrate:  0.712

ADMET: Excretion

Clearance (CL):  7.468
Half-life (T1/2):  0.678

ADMET: Toxicity

hERG Blockers:  0.466
Human Hepatotoxicity (H-HT):  0.953
Drug-inuced Liver Injury (DILI):  0.838
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.933
Maximum Recommended Daily Dose:  0.975
Skin Sensitization:  0.133
Carcinogencity:  0.035
Eye Corrosion:  0.004
Eye Irritation:  0.037
Respiratory Toxicity:  0.973

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  Natural Product: NPC244016

Natural Product ID:  NPC244016
Common Name*:   KWOLFJPFCHCOCG-VIQYUKPQSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KWOLFJPFCHCOCG-VIQYUKPQSA-N
Standard InCHI:  InChI=1S/C8H8O/c1-7(9)8-5-3-2-4-6-8/h2-6H,1H3/i2D,3D,4D,5D,6D
SMILES:  CC(=O)c1c(c(c(c(c1[2H])[2H])[2H])[2H])[2H]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11457690
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003670] Aryl ketones
              • [CHEMONTID:0004296] Phenylketones
                • [CHEMONTID:0004298] Alkyl-phenylketones

*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
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[1402962]
NPO31390 Cynanchum paniculatum Species Apocynaceae Eukaryota roots n.a. n.a. PMID[14738392]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. root n.a. PMID[18975262]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. PMID[24333010]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. PMID[25565282]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota Buds n.a. n.a. PMID[25927817]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota Mycelia n.a. n.a. PMID[26807743]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Flower Buds n.a. n.a. PMID[26977531]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota Fruiting Bodies n.a. n.a. PMID[33246107]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[8904847]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO10256 Liquidambar orientalis Species Altingiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23017 Urtica dioica Species Urticaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11291 Styrax benzoin Species Styracaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14105.2 Panax pseudo-ginseng var. notoginseng Varieties Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27864 Resina liquidambaris n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31390 Cynanchum paniculatum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14148.1 Panax pseudo - ginseng var. notoginseng Varieties Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10256 Liquidambar orientalis Species Altingiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24694 Vincetoxicum pycnostelma Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11291 Styrax benzoin Species Styracaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14105.2 Panax pseudo-ginseng var. notoginseng Varieties Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27864 Resina liquidambaris n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO16841 Elsholtzia bodinieri Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23017 Urtica dioica Species Urticaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10256 Liquidambar orientalis Species Altingiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23017 Urtica dioica Species Urticaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31390 Cynanchum paniculatum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11291 Styrax benzoin Species Styracaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10256 Liquidambar orientalis Species Altingiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11291 Styrax benzoin Species Styracaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24694 Vincetoxicum pycnostelma Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21410 Populus balsamifera Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11291 Styrax benzoin Species Styracaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16841 Elsholtzia bodinieri Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10256 Liquidambar orientalis Species Altingiaceae 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 NPC244016 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 NPC244016 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