Structure

Physi-Chem Properties

Molecular Weight:  478.13
Volume:  465.581
LogP:  4.0
LogD:  2.847
LogS:  -5.329
# Rotatable Bonds:  6
TPSA:  113.66
# H-Bond Aceptor:  9
# H-Bond Donor:  1
# Rings:  5
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.334
Synthetic Accessibility Score:  3.565
Fsp3:  0.231
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.789
MDCK Permeability:  5.1043629355262965e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.075
Plasma Protein Binding (PPB):  84.0057601928711%
Volume Distribution (VD):  0.963
Pgp-substrate:  14.866000175476074%

ADMET: Metabolism

CYP1A2-inhibitor:  0.233
CYP1A2-substrate:  0.89
CYP2C19-inhibitor:  0.914
CYP2C19-substrate:  0.209
CYP2C9-inhibitor:  0.904
CYP2C9-substrate:  0.791
CYP2D6-inhibitor:  0.83
CYP2D6-substrate:  0.583
CYP3A4-inhibitor:  0.803
CYP3A4-substrate:  0.525

ADMET: Excretion

Clearance (CL):  1.849
Half-life (T1/2):  0.478

ADMET: Toxicity

hERG Blockers:  0.069
Human Hepatotoxicity (H-HT):  0.6
Drug-inuced Liver Injury (DILI):  0.966
AMES Toxicity:  0.525
Rat Oral Acute Toxicity:  0.653
Maximum Recommended Daily Dose:  0.837
Skin Sensitization:  0.7
Carcinogencity:  0.413
Eye Corrosion:  0.003
Eye Irritation:  0.163
Respiratory Toxicity:  0.044

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General Info & Identifiers & Properties  
Structure MOL file  
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Similar NPs/Drugs  

  Natural Product: NPC126737

Natural Product ID:  NPC126737
Common Name*:   SJURZXHCGJQOET-FYYLOGMGSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SJURZXHCGJQOET-FYYLOGMGSA-N
Standard InCHI:  InChI=1S/C26H22O9/c1-13(27)32-12-21-23(14-8-15(28)10-16(9-14)30-2)35-25-20(31-3)11-18-22(29)17-6-4-5-7-19(17)33-24(18)26(25)34-21/h4-11,21,23,28H,12H2,1-3H3/t21-,23-/m1/s1
SMILES:  CC(=O)OC[C@@H]1[C@@H](c2cc(cc(c2)OC)O)Oc2c(cc3c(=O)c4ccccc4oc3c2O1)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002699] Benzodioxanes
        • [CHEMONTID:0002704] Phenylbenzodioxanes
          • [CHEMONTID:0002707] Phenylbenzo-1,4-dioxanes

*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
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[11473425]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[11975482]
NPO22748 Neophaeosphaeria quadriseptata Species Leptosphaeriaceae Eukaryota n.a. n.a. n.a. PMID[16499313]
NPO24232 Boehmeria pannosa Species Urticaceae Eukaryota roots n.a. n.a. PMID[16872154]
NPO26529 Hypericum oblongifolium Species Hypericaceae Eukaryota n.a. whole plant n.a. PMID[16880649]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. leaf n.a. PMID[17401878]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. stem n.a. PMID[17401878]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. root n.a. PMID[17401878]
NPO26234 Annona muricata Species Annonaceae Eukaryota Leaves n.a. n.a. PMID[7494150]
NPO26234 Annona muricata Species Annonaceae Eukaryota Leaves n.a. n.a. PMID[7673926]
NPO26234 Annona muricata Species Annonaceae Eukaryota Leaves n.a. n.a. PMID[7673935]
NPO26234 Annona muricata Species Annonaceae Eukaryota Leaves n.a. n.a. PMID[7673936]
NPO26234 Annona muricata Species Annonaceae Eukaryota leaves n.a. n.a. PMID[8946744]
NPO26234 Annona muricata Species Annonaceae Eukaryota seeds n.a. n.a. PMID[8991944]
NPO26234 Annona muricata Species Annonaceae Eukaryota Leaves n.a. n.a. PMID[9584396]
NPO26234 Annona muricata Species Annonaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26529 Hypericum oblongifolium Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25812 Dipentodon sinicus Species Dipentodontaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24232 Boehmeria pannosa Species Urticaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3170 Piper lanceifolium Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22748 Neophaeosphaeria quadriseptata Species Leptosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26315 Trikentrion flabelliforme Species Raspailiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4308 Pericome caudata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25943 Cirsium carolinianum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26234 Annona muricata Species Annonaceae 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 NPC126737 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 NPC126737 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