Structure

Physi-Chem Properties

Molecular Weight:  468.4
Volume:  531.553
LogP:  7.988
LogD:  5.782
LogS:  -6.81
# Rotatable Bonds:  6
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.298
Synthetic Accessibility Score:  5.398
Fsp3:  0.906
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.969
MDCK Permeability:  1.0848933015950024e-05
Pgp-inhibitor:  0.008
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.991
30% Bioavailability (F30%):  0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.021
Plasma Protein Binding (PPB):  92.42931365966797%
Volume Distribution (VD):  1.515
Pgp-substrate:  1.3097947835922241%

ADMET: Metabolism

CYP1A2-inhibitor:  0.043
CYP1A2-substrate:  0.148
CYP2C19-inhibitor:  0.143
CYP2C19-substrate:  0.939
CYP2C9-inhibitor:  0.248
CYP2C9-substrate:  0.44
CYP2D6-inhibitor:  0.093
CYP2D6-substrate:  0.317
CYP3A4-inhibitor:  0.718
CYP3A4-substrate:  0.501

ADMET: Excretion

Clearance (CL):  4.68
Half-life (T1/2):  0.021

ADMET: Toxicity

hERG Blockers:  0.886
Human Hepatotoxicity (H-HT):  0.333
Drug-inuced Liver Injury (DILI):  0.397
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.035
Maximum Recommended Daily Dose:  0.699
Skin Sensitization:  0.971
Carcinogencity:  0.084
Eye Corrosion:  0.658
Eye Irritation:  0.568
Respiratory Toxicity:  0.772

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

  Natural Product: NPC174423

Natural Product ID:  NPC174423
Common Name*:   PQNTWKDHNSWVPU-XMZAIMIDSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PQNTWKDHNSWVPU-XMZAIMIDSA-N
Standard InCHI:  InChI=1S/C32H52O2/c1-21(2)10-9-11-22(3)24-14-16-30(8)26-13-12-25-28(5,6)27(34-23(4)33)15-17-31(25)20-32(26,31)19-18-29(24,30)7/h10,22,24-27H,9,11-20H2,1-8H3/t22-,24+,25+,26+,27-,29+,30+,31+,32-/m0/s1
SMILES:  CC(=CCC[C@H](C)[C@H]1CC[C@]2(C)[C@H]3CC[C@@H]4C(C)(C)[C@H](CC[C@]54C[C@@]35CC[C@]12C)OC(=O)C)C
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:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0002321] Cycloartanols and derivatives

*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
NPO17048 Jungermannia subulata Species Jungermanniaceae Eukaryota n.a. n.a. n.a. PMID[11999396]
NPO16027 Niphogeton ternata Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18366 Papaver commutatum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18366 Papaver commutatum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16027 Niphogeton ternata Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15580 Justicia simplex Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18366 Papaver commutatum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15580 Justicia simplex Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17933 Cylicodaphne sebifera n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO17488 Rhoiptelea chiliantha Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17048 Jungermannia subulata Species Jungermanniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18903 Chromodoris willani Species Chromodorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17264 Mycena haematopus Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18366 Papaver commutatum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18434 Dactylosporangium aurantiacum Species Micromonosporaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17168 Ageratina riparia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16942 Asparagus thunbergianus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18044 Lotus albus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11999 Piptadenia peregrina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16027 Niphogeton ternata Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16421 Chalciporus piperatus Species Boletaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5062 Aristolochia tagala Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2066 Streptomyces ipomoeae Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO7166 Streptomyces aureus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO15832 Ruscus hypophyllum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13892 Calea clausseniana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16631 Libocedrus yateensis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15580 Justicia simplex Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO426 Camellia reticulata Species Theaceae 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 NPC174423 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 NPC174423 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