Structure

Physi-Chem Properties

Molecular Weight:  264.14
Volume:  269.578
LogP:  1.562
LogD:  1.139
LogS:  -2.381
# Rotatable Bonds:  0
TPSA:  63.6
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.673
Synthetic Accessibility Score:  4.624
Fsp3:  0.733
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:  -4.612
MDCK Permeability:  7.223591819638386e-05
Pgp-inhibitor:  0.78
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.046
30% Bioavailability (F30%):  0.042

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.944
Plasma Protein Binding (PPB):  51.77561950683594%
Volume Distribution (VD):  0.805
Pgp-substrate:  47.95687484741211%

ADMET: Metabolism

CYP1A2-inhibitor:  0.031
CYP1A2-substrate:  0.701
CYP2C19-inhibitor:  0.03
CYP2C19-substrate:  0.766
CYP2C9-inhibitor:  0.014
CYP2C9-substrate:  0.053
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.052
CYP3A4-inhibitor:  0.75
CYP3A4-substrate:  0.428

ADMET: Excretion

Clearance (CL):  8.502
Half-life (T1/2):  0.188

ADMET: Toxicity

hERG Blockers:  0.037
Human Hepatotoxicity (H-HT):  0.378
Drug-inuced Liver Injury (DILI):  0.134
AMES Toxicity:  0.021
Rat Oral Acute Toxicity:  0.937
Maximum Recommended Daily Dose:  0.545
Skin Sensitization:  0.404
Carcinogencity:  0.866
Eye Corrosion:  0.163
Eye Irritation:  0.162
Respiratory Toxicity:  0.958

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

  Natural Product: NPC91413

Natural Product ID:  NPC91413
Common Name*:   NGPDZEACIWDCKX-DHKWMEDESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NGPDZEACIWDCKX-DHKWMEDESA-N
Standard InCHI:  InChI=1S/C15H20O4/c1-8-9-4-6-14(2)10(16)5-7-15(3,18)12(14)11(9)19-13(8)17/h5,7-9,11-12,18H,4,6H2,1-3H3/t8-,9-,11-,12+,14-,15-/m0/s1
SMILES:  C[C@H]1[C@@H]2CC[C@@]3(C)C(=O)C=C[C@@](C)([C@@H]3[C@H]2OC1=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   12443235
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001543] Sesquiterpene lactones
            • [CHEMONTID:0001772] Eudesmanolides, secoeudesmanolides, 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
NPO19178 Justicia hyssopifolia Species Acanthaceae Eukaryota n.a. n.a. n.a. PMID[11312930]
NPO14250 Schisandra henryi Species Schisandraceae Eukaryota n.a. stem n.a. PMID[14661856]
NPO15563 Valeriana prionophylla Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[15270567]
NPO2890 Scrophularia lepidota Species Scrophulariaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO16933 Halichondria cylindrata Species Halichondriidae Eukaryota n.a. n.a. n.a. PMID[8991950]
NPO13812 Illicium floridanum Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[9548851]
NPO2890 Scrophularia lepidota Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19178 Justicia hyssopifolia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2890 Scrophularia lepidota Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19178 Justicia hyssopifolia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14250 Schisandra henryi Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14250 Schisandra henryi Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15563 Valeriana prionophylla Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14250 Schisandra henryi Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23695 Setosphaeria turcica Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18294 Anacyclus clavatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18226 Ajuga chia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10635 Schkuhria pusilla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12395 Cardamine impatiens Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15831 Panicum dichotomiflorum Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17818 Acrantophis dumerili Species Boidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16046 Buchnerodendron speciosum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO18565 Penicillium striatisporum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14245.1 Veratrum album subsp. lobelianum Subspecies Melanthiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16933 Halichondria cylindrata Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26926 Montanoa frutescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18501 Salvia carduacea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18969 Dysidea etheria Species Dysideidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21638 Attalea cohune Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13812 Illicium floridanum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16268 Blattella germanica Species Ectobiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18776 Erlangea fusca Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27137 Ocotea usambarensis Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19178 Justicia hyssopifolia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18627 Cardamine komarovii Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22448 Helichrysum nanum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2890 Scrophularia lepidota Species Scrophulariaceae 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 NPC91413 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 NPC91413 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