Structure

Physi-Chem Properties

Molecular Weight:  315.11
Volume:  301.572
LogP:  1.549
LogD:  1.62
LogS:  -3.009
# Rotatable Bonds:  0
TPSA:  68.23
# H-Bond Aceptor:  6
# H-Bond Donor:  1
# Rings:  5
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.57
Synthetic Accessibility Score:  4.19
Fsp3:  0.471
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:  -4.632
MDCK Permeability:  5.13090672029648e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.09
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.014
30% Bioavailability (F30%):  0.946

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.988
Plasma Protein Binding (PPB):  65.19210052490234%
Volume Distribution (VD):  2.433
Pgp-substrate:  42.54042053222656%

ADMET: Metabolism

CYP1A2-inhibitor:  0.711
CYP1A2-substrate:  0.647
CYP2C19-inhibitor:  0.122
CYP2C19-substrate:  0.818
CYP2C9-inhibitor:  0.059
CYP2C9-substrate:  0.583
CYP2D6-inhibitor:  0.949
CYP2D6-substrate:  0.774
CYP3A4-inhibitor:  0.693
CYP3A4-substrate:  0.333

ADMET: Excretion

Clearance (CL):  15.121
Half-life (T1/2):  0.396

ADMET: Toxicity

hERG Blockers:  0.056
Human Hepatotoxicity (H-HT):  0.132
Drug-inuced Liver Injury (DILI):  0.139
AMES Toxicity:  0.061
Rat Oral Acute Toxicity:  0.899
Maximum Recommended Daily Dose:  0.917
Skin Sensitization:  0.038
Carcinogencity:  0.866
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.949

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  Natural Product: NPC300240

Natural Product ID:  NPC300240
Common Name*:   DGQPIOQRPAGNGB-KDMZPGMDSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DGQPIOQRPAGNGB-KDMZPGMDSA-N
Standard InCHI:  InChI=1S/C17H17NO5/c1-18-3-2-8-4-11(19)16-14(15(8)18)9-5-12-13(22-7-21-12)6-10(9)17(20)23-16/h4-6,11,14-16,19H,2-3,7H2,1H3/t11-,14-,15?,16+/m0/s1
SMILES:  CN1CCC2=C[C@@H]([C@@H]3[C@@H](c4cc5c(cc4C(=O)O3)OCO5)C12)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10358316
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0001775] Amaryllidaceae alkaloids
        • [CHEMONTID:0004122] Homolycorine-type amaryllidaceae alkaloids

*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
NPO22821 Chamaecyparis obtusa Species Cupressaceae Eukaryota n.a. heartwood n.a. DOI[10.1007/s10086-012-1280-8]
NPO23239 Amaryllis belladonna Species Amaryllidaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/ja01076a047]
NPO27517 Crinum latifolium Species Amaryllidaceae Eukaryota n.a. leaf n.a. PMID[15595606]
NPO22821 Chamaecyparis obtusa Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[16540181]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota rhizomes n.a. n.a. PMID[19757853]
NPO9927.2 Crinum asiaticum var. sinicum Varieties Amaryllidaceae Eukaryota n.a. leaf n.a. PMID[21314165]
NPO9927.2 Crinum asiaticum var. sinicum Varieties Amaryllidaceae Eukaryota n.a. bulb n.a. PMID[21314165]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. rhizome n.a. PMID[21370894]
NPO27843 Lycoris radiata Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[21510636]
NPO16709 Clivia miniata Species Amaryllidaceae Eukaryota n.a. leaf n.a. PMID[24221429]
NPO23239 Amaryllis belladonna Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[6512532]
NPO16709 Clivia miniata Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[7153775]
NPO22317 Crinum amabile Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[8229016]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota Rhizomes n.a. n.a. PMID[8482946]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9927.2 Crinum asiaticum var. sinicum Varieties Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22821 Chamaecyparis obtusa Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16709 Clivia miniata Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22317 Crinum amabile Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27843 Lycoris radiata Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23239 Amaryllis belladonna Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9927 Crinum asiaticum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27517 Crinum latifolium Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9927.2 Crinum asiaticum var. sinicum Varieties Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22317 Crinum amabile Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22821 Chamaecyparis obtusa Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16709 Clivia miniata Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27843 Lycoris radiata Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27517 Crinum latifolium Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23239 Amaryllis belladonna Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9927 Crinum asiaticum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23239 Amaryllis belladonna Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27843 Lycoris radiata Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27843 Lycoris radiata Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9927 Crinum asiaticum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23239 Amaryllis belladonna Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26741 Anemarrhena asphodeloides Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22821 Chamaecyparis obtusa Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27517 Crinum latifolium Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22317 Crinum amabile Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16709 Clivia miniata Species Amaryllidaceae 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 NPC300240 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 NPC300240 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