Structure

Physi-Chem Properties

Molecular Weight:  328.18
Volume:  338.136
LogP:  2.097
LogD:  1.993
LogS:  -2.61
# Rotatable Bonds:  3
TPSA:  64.79
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.862
Synthetic Accessibility Score:  4.233
Fsp3:  0.526
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:  -4.675
MDCK Permeability:  1.0634432328515686e-05
Pgp-inhibitor:  0.007
Pgp-substrate:  0.991
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.389
30% Bioavailability (F30%):  0.02

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.815
Plasma Protein Binding (PPB):  47.830162048339844%
Volume Distribution (VD):  1.77
Pgp-substrate:  57.919639587402344%

ADMET: Metabolism

CYP1A2-inhibitor:  0.026
CYP1A2-substrate:  0.461
CYP2C19-inhibitor:  0.028
CYP2C19-substrate:  0.895
CYP2C9-inhibitor:  0.036
CYP2C9-substrate:  0.209
CYP2D6-inhibitor:  0.085
CYP2D6-substrate:  0.432
CYP3A4-inhibitor:  0.158
CYP3A4-substrate:  0.904

ADMET: Excretion

Clearance (CL):  12.615
Half-life (T1/2):  0.114

ADMET: Toxicity

hERG Blockers:  0.071
Human Hepatotoxicity (H-HT):  0.307
Drug-inuced Liver Injury (DILI):  0.113
AMES Toxicity:  0.917
Rat Oral Acute Toxicity:  0.168
Maximum Recommended Daily Dose:  0.94
Skin Sensitization:  0.05
Carcinogencity:  0.945
Eye Corrosion:  0.003
Eye Irritation:  0.011
Respiratory Toxicity:  0.933

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

  Natural Product: NPC32378

Natural Product ID:  NPC32378
Common Name*:   PANDVJNMJNDSCF-LIRRHRJNSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PANDVJNMJNDSCF-LIRRHRJNSA-N
Standard InCHI:  InChI=1S/C19H24N2O3/c1-23-14-4-3-13-6-8-21-7-5-12-9-17(24-2)15(18(20)22)10-16(12)19(13,21)11-14/h3,9-10,14H,4-8,11H2,1-2H3,(H2,20,22)/t14-,19-/m0/s1
SMILES:  CO[C@H]1CC=C2CCN3CCc4cc(c(cc4[C@]23C1)C(=N)O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0001782] Erythrina alkaloids
        • [CHEMONTID:0002780] Erythrinanes

*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
NPO27739 Erythrina mildbraedii Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0031-9422(88)80746-5]
NPO27686 Aglaia odorata Species Meliaceae Eukaryota n.a. leaf n.a. DOI[10.1016/S0031-9422(00)94986-0]
NPO25388 Siliquariaspongia japonica n.a. n.a. n.a. n.a. n.a. n.a. PMID[10425118]
NPO12170 Solanum indicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[11575964]
NPO27931 Caulerpa taxifolia Species Caulerpaceae Eukaryota n.a. n.a. n.a. PMID[16563751]
NPO27739 Erythrina mildbraedii Species Fabaceae Eukaryota root bark Buea, Southwest Province, Cameroon 1997-JUL PMID[17125223]
NPO27686 Aglaia odorata Species Meliaceae Eukaryota n.a. flower n.a. PMID[17679444]
NPO27646 Cystoseira baccata Species Sargassaceae Eukaryota n.a. n.a. n.a. PMID[18980381]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota n.a. fruit n.a. PMID[23132311]
NPO27686 Aglaia odorata Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[8759160]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota n.a. n.a. Database[FooDB]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota Fruits n.a. Database[FooDB]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27803 Cercidiphyllum japonicum Species Cercidiphyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27686 Aglaia odorata Species Meliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27666 Sophora tetraptera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27803 Cercidiphyllum japonicum Species Cercidiphyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12170 Solanum indicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27666 Sophora tetraptera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27686 Aglaia odorata Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27666 Sophora tetraptera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27803 Cercidiphyllum japonicum Species Cercidiphyllaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27686 Aglaia odorata Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27869 Bombacopsis glabra n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO27522 Gongronella urceolifera Species Cunninghamellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27976 Astragalus wootoni Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27726 Diplocarpon mali Species Dermateaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27686 Aglaia odorata Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27931 Caulerpa taxifolia Species Caulerpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27703 Eclipta erecta Species Cerambycidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27646 Cystoseira baccata Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27838 Rebutia marsoneri Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27803 Cercidiphyllum japonicum Species Cercidiphyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27468 Rhizopogon roseolus Species Rhizopogonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27739 Erythrina mildbraedii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27216 Oreodaphne porosa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO12170 Solanum indicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25388 Siliquariaspongia japonica n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO18354 Meiothermus ruber Species Thermaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO26332 Ramalina tumidula Species Ramalinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27617 Phoenix dactylifera Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27666 Sophora tetraptera Species Fabaceae 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 NPC32378 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 NPC32378 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