Structure

Physi-Chem Properties

Molecular Weight:  396.18
Volume:  388.583
LogP:  0.157
LogD:  -0.056
LogS:  -1.688
# Rotatable Bonds:  5
TPSA:  136.68
# H-Bond Aceptor:  8
# H-Bond Donor:  5
# Rings:  3
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.451
Synthetic Accessibility Score:  4.348
Fsp3:  0.65
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:  -5.339
MDCK Permeability:  1.0430847396492027e-05
Pgp-inhibitor:  0.008
Pgp-substrate:  0.856
Human Intestinal Absorption (HIA):  0.875
20% Bioavailability (F20%):  0.038
30% Bioavailability (F30%):  0.558

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.153
Plasma Protein Binding (PPB):  78.83234405517578%
Volume Distribution (VD):  1.534
Pgp-substrate:  14.936527252197266%

ADMET: Metabolism

CYP1A2-inhibitor:  0.035
CYP1A2-substrate:  0.255
CYP2C19-inhibitor:  0.019
CYP2C19-substrate:  0.746
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.116
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.133
CYP3A4-inhibitor:  0.014
CYP3A4-substrate:  0.17

ADMET: Excretion

Clearance (CL):  1.303
Half-life (T1/2):  0.493

ADMET: Toxicity

hERG Blockers:  0.039
Human Hepatotoxicity (H-HT):  0.245
Drug-inuced Liver Injury (DILI):  0.423
AMES Toxicity:  0.434
Rat Oral Acute Toxicity:  0.044
Maximum Recommended Daily Dose:  0.013
Skin Sensitization:  0.101
Carcinogencity:  0.024
Eye Corrosion:  0.003
Eye Irritation:  0.02
Respiratory Toxicity:  0.031

Download Data

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

  Natural Product: NPC34771

Natural Product ID:  NPC34771
Common Name*:   IBIIWSKOZHHITE-CYBMUJFWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  IBIIWSKOZHHITE-CYBMUJFWSA-N
Standard InCHI:  InChI=1S/C15H20O4/c1-8-6-10-12(11(7-17)9(8)4-5-16)14(19)15(2,3)13(10)18/h6,13,16-18H,4-5,7H2,1-3H3/t13-/m1/s1
SMILES:  Cc1cc2c(c(CO)c1CCO)C(=O)C(C)(C)[C@@H]2O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   90474163
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000027] Indanes
        • [CHEMONTID:0001151] Indanones

*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
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[10556916]
NPO19369 Bacillus thuringiensis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[11087590]
NPO26770 Pteris multifida Species Pteridaceae Eukaryota Whole plant n.a. n.a. PMID[18181575]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[19406895]
NPO3494 Swietenia mahagoni Species Meliaceae Eukaryota fruits n.a. n.a. PMID[19902967]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[19917748]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[20932054]
NPO14077 Chamaecyparis lawsoniana Species Cupressaceae Eukaryota n.a. leaf n.a. PMID[23157017]
NPO14077 Chamaecyparis lawsoniana Species Cupressaceae Eukaryota n.a. stem n.a. PMID[23157017]
NPO11601 Chandonanthus hirtellus Species Anastrophyllaceae Eukaryota n.a. Chinese liverworts n.a. PMID[24491225]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[25043228]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[25960261]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Europe PMC[305622]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[32603106]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. Antarctic n.a. PMID[8882433]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26770 Pteris multifida Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2756 Emerita analoga Species Hippidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15094 Coriaria myrtifolia Species Coriariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18407 Pteris fauriei Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2756 Emerita analoga Species Hippidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26770 Pteris multifida Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3494 Swietenia mahagoni Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16170 Xerula longipes Species Physalacriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8866 Papaver atlanticum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2312 Encephalosphaera lasiandra Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2756 Emerita analoga Species Hippidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15306 Smilax japonica Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15818 Lycianthes marlipoensis Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11567 Picradeniopsis absinthifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18407 Pteris fauriei Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15094 Coriaria myrtifolia Species Coriariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1890 Lidbeckia pectinata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12294 Kydia calycina Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12517 Tylophora cordifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27787 Pseudocentrotus depressus Species Echinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10624 Solidago wrightii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15726 Rudbeckia subtomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14630 Boronia ramosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8611 Cornutia grandifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19369 Bacillus thuringiensis Species Bacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO14077 Chamaecyparis lawsoniana Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26770 Pteris multifida Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7056 Pedinophyllum interruptum Species Plagiochilaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9155 Kageneckia angustifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13236 Viguiera multiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11601 Chandonanthus hirtellus Species Anastrophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13360 Passiflora racemosa Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO7868 Xeromphis obovata n.a. n.a. n.a. 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
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 119600.0 nM PMID[456336]

☑ 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 NPC34771 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 NPC34771 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