Structure

Physi-Chem Properties

Molecular Weight:  234.13
Volume:  249.412
LogP:  1.604
LogD:  1.376
LogS:  -2.519
# Rotatable Bonds:  2
TPSA:  57.53
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.819
Synthetic Accessibility Score:  3.532
Fsp3:  0.5
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:  -4.656
MDCK Permeability:  1.0348725481890142e-05
Pgp-inhibitor:  0.004
Pgp-substrate:  0.076
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.865
30% Bioavailability (F30%):  0.073

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.706
Plasma Protein Binding (PPB):  68.47537994384766%
Volume Distribution (VD):  0.932
Pgp-substrate:  29.254653930664062%

ADMET: Metabolism

CYP1A2-inhibitor:  0.523
CYP1A2-substrate:  0.885
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.839
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.502
CYP2D6-inhibitor:  0.035
CYP2D6-substrate:  0.327
CYP3A4-inhibitor:  0.054
CYP3A4-substrate:  0.55

ADMET: Excretion

Clearance (CL):  7.183
Half-life (T1/2):  0.196

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.157
Drug-inuced Liver Injury (DILI):  0.455
AMES Toxicity:  0.145
Rat Oral Acute Toxicity:  0.109
Maximum Recommended Daily Dose:  0.275
Skin Sensitization:  0.141
Carcinogencity:  0.055
Eye Corrosion:  0.004
Eye Irritation:  0.169
Respiratory Toxicity:  0.299

Download Data

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

  Natural Product: NPC135654

Natural Product ID:  NPC135654
Common Name*:   QQPCNRKHGFIVLH-RNCFNFMXSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QQPCNRKHGFIVLH-RNCFNFMXSA-N
Standard InCHI:  InChI=1S/C14H18O3/c1-7-6-11-12(8(2)10(7)4-5-15)14(17)9(3)13(11)16/h6,9,13,15-16H,4-5H2,1-3H3/t9-,13+/m1/s1
SMILES:  Cc1cc2c(c(C)c1CCO)C(=O)[C@H](C)[C@@H]2O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   46850077
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. stem n.a. PMID[23157017]
NPO14077 Chamaecyparis lawsoniana Species Cupressaceae Eukaryota n.a. leaf 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]
NPO27620 Pteris cretica Species Pteridaceae Eukaryota n.a. n.a. n.a. PMID[28006909]
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]
NPO2756 Emerita analoga Species Hippidae Eukaryota n.a. n.a. n.a. Database[HerDing]
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]
NPO27620 Pteris cretica 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]
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]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
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]
NPO27620 Pteris cretica Species Pteridaceae 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]
NPO16170 Xerula longipes Species Physalacriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3494 Swietenia mahagoni Species Meliaceae 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]
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]
NPO12517 Tylophora cordifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12294 Kydia calycina Species Malvaceae 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
NPT2615 Cell Line HEK-293T Homo sapiens Activity = 100.0 % PMID[28006909]
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 253200.0 nM PMID[28532669]

☑ 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 NPC135654 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 NPC135654 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