Structure

Physi-Chem Properties

Molecular Weight:  479.31
Volume:  522.74
LogP:  5.707
LogD:  4.004
LogS:  -4.521
# Rotatable Bonds:  9
TPSA:  74.43
# H-Bond Aceptor:  6
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.391
Synthetic Accessibility Score:  4.935
Fsp3:  0.517
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.831
MDCK Permeability:  1.3666290215041954e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.822
Human Intestinal Absorption (HIA):  0.076
20% Bioavailability (F20%):  0.521
30% Bioavailability (F30%):  0.207

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.687
Plasma Protein Binding (PPB):  93.93940734863281%
Volume Distribution (VD):  1.239
Pgp-substrate:  5.883066177368164%

ADMET: Metabolism

CYP1A2-inhibitor:  0.398
CYP1A2-substrate:  0.227
CYP2C19-inhibitor:  0.939
CYP2C19-substrate:  0.381
CYP2C9-inhibitor:  0.901
CYP2C9-substrate:  0.504
CYP2D6-inhibitor:  0.924
CYP2D6-substrate:  0.704
CYP3A4-inhibitor:  0.936
CYP3A4-substrate:  0.648

ADMET: Excretion

Clearance (CL):  2.718
Half-life (T1/2):  0.264

ADMET: Toxicity

hERG Blockers:  0.428
Human Hepatotoxicity (H-HT):  0.763
Drug-inuced Liver Injury (DILI):  0.411
AMES Toxicity:  0.067
Rat Oral Acute Toxicity:  0.324
Maximum Recommended Daily Dose:  0.894
Skin Sensitization:  0.618
Carcinogencity:  0.197
Eye Corrosion:  0.003
Eye Irritation:  0.011
Respiratory Toxicity:  0.687

Download Data

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

  Natural Product: NPC191259

Natural Product ID:  NPC191259
Common Name*:   WUGMGNWGTQDXDH-NVLPUFGLSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WUGMGNWGTQDXDH-NVLPUFGLSA-N
Standard InCHI:  InChI=1S/C29H41N3O3/c1-9-29(7,14-10-11-18(2)3)23-12-13-24-25-21(16-30-26(23)25)15-22(17-35-20(6)33)31-28(34)27(19(4)5)32(24)8/h9,11-13,16,19,22,27,30H,1,10,14-15,17H2,2-8H3,(H,31,34)/t22-,27-,29-/m0/s1
SMILES:  C=C[C@@](C)(CCC=C(C)C)c1ccc2c3c(C[C@@H](COC(=O)C)N=C([C@H](C(C)C)N2C)O)c[nH]c13
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10096667
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0002309] Alpha amino acid amides

*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
NPO11600 Scolopendra subspinipes Species Scolopendridae Eukaryota n.a. n.a. n.a. DOI[10.1021/np960188t]
NPO16759 Polyalthia debilis Species Annonaceae Eukaryota n.a. root n.a. PMID[12762793]
NPO11600 Scolopendra subspinipes Species Scolopendridae Eukaryota n.a. n.a. n.a. PMID[16595909]
NPO12302 Hebanthe paniculata Species Amaranthaceae Eukaryota n.a. root n.a. PMID[19941264]
NPO16759 Polyalthia debilis Species Annonaceae Eukaryota Roots n.a. n.a. PMID[20795741]
NPO11600 Scolopendra subspinipes Species Scolopendridae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12302 Hebanthe paniculata Species Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12135 Rhamnus triquetra Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11600 Scolopendra subspinipes Species Scolopendridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3396 Allium cernuum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16176 Citrus fusca Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16759 Polyalthia debilis Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15140 Soja max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21487 Eunicea flexuosa Species Plexauridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13233 Solanum megacarpum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12302 Hebanthe paniculata Species Amaranthaceae 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 NPC191259 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 NPC191259 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