Structure

Physi-Chem Properties

Molecular Weight:  320.27
Volume:  355.127
LogP:  4.443
LogD:  4.327
LogS:  -4.777
# Rotatable Bonds:  0
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.695
Synthetic Accessibility Score:  5.754
Fsp3:  1.0
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:  -4.799
MDCK Permeability:  2.5126317268586718e-05
Pgp-inhibitor:  0.44
Pgp-substrate:  0.034
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.087
30% Bioavailability (F30%):  0.342

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.125
Plasma Protein Binding (PPB):  92.35762023925781%
Volume Distribution (VD):  1.338
Pgp-substrate:  6.774627208709717%

ADMET: Metabolism

CYP1A2-inhibitor:  0.047
CYP1A2-substrate:  0.14
CYP2C19-inhibitor:  0.042
CYP2C19-substrate:  0.803
CYP2C9-inhibitor:  0.26
CYP2C9-substrate:  0.305
CYP2D6-inhibitor:  0.016
CYP2D6-substrate:  0.373
CYP3A4-inhibitor:  0.213
CYP3A4-substrate:  0.201

ADMET: Excretion

Clearance (CL):  6.375
Half-life (T1/2):  0.206

ADMET: Toxicity

hERG Blockers:  0.039
Human Hepatotoxicity (H-HT):  0.228
Drug-inuced Liver Injury (DILI):  0.039
AMES Toxicity:  0.012
Rat Oral Acute Toxicity:  0.94
Maximum Recommended Daily Dose:  0.993
Skin Sensitization:  0.921
Carcinogencity:  0.05
Eye Corrosion:  0.936
Eye Irritation:  0.932
Respiratory Toxicity:  0.961

Download Data

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

  Natural Product: NPC213234

Natural Product ID:  NPC213234
Common Name*:   PUXYTTAHRHRAMN-WIKSGOJNSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PUXYTTAHRHRAMN-WIKSGOJNSA-N
Standard InCHI:  InChI=1S/C21H36O2/c1-18(2)11-14(22)12-20(5)15(18)8-9-21-10-13(6-7-16(20)21)19(3,4)17(21)23/h13-17,22-23H,6-12H2,1-5H3/t13-,14-,15-,16+,17+,20-,21-/m1/s1
SMILES:  CC1(C)C[C@H](C[C@]2(C)[C@@H]1CC[C@@]13C[C@@H](CC[C@@H]21)C(C)(C)[C@@H]3O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0003782] Kaurane 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
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]
NPO26770 Pteris multifida Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2756 Emerita analoga Species Hippidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2756 Emerita analoga Species Hippidae 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]
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]
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]
NPO10624 Solidago wrightii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8611 Cornutia grandifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27787 Pseudocentrotus depressus Species Echinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14630 Boronia ramosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14077 Chamaecyparis lawsoniana Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15726 Rudbeckia subtomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7056 Pedinophyllum interruptum Species Plagiochilaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19369 Bacillus thuringiensis Species Bacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11601 Chandonanthus hirtellus Species Anastrophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26770 Pteris multifida Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13236 Viguiera multiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9155 Kageneckia angustifolia Species Rosaceae Eukaryota 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]
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]
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]
NPO16170 Xerula longipes Species Physalacriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2756 Emerita analoga Species Hippidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2312 Encephalosphaera lasiandra Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15306 Smilax japonica Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11567 Picradeniopsis absinthifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15818 Lycianthes marlipoensis Species Solanaceae 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 NPC213234 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 NPC213234 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