Structure

Physi-Chem Properties

Molecular Weight:  362.12
Volume:  319.036
LogP:  -1.765
LogD:  -1.265
LogS:  -1.855
# Rotatable Bonds:  4
TPSA:  161.6
# H-Bond Aceptor:  10
# H-Bond Donor:  6
# Rings:  4
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.276
Synthetic Accessibility Score:  5.091
Fsp3:  0.867
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:  -6.313
MDCK Permeability:  0.00013538084749598056
Pgp-inhibitor:  0.0
Pgp-substrate:  0.99
Human Intestinal Absorption (HIA):  0.916
20% Bioavailability (F20%):  0.64
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.22
Plasma Protein Binding (PPB):  27.611492156982422%
Volume Distribution (VD):  0.369
Pgp-substrate:  57.17479705810547%

ADMET: Metabolism

CYP1A2-inhibitor:  0.011
CYP1A2-substrate:  0.037
CYP2C19-inhibitor:  0.012
CYP2C19-substrate:  0.394
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.037
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.099
CYP3A4-inhibitor:  0.015
CYP3A4-substrate:  0.022

ADMET: Excretion

Clearance (CL):  1.342
Half-life (T1/2):  0.815

ADMET: Toxicity

hERG Blockers:  0.099
Human Hepatotoxicity (H-HT):  0.836
Drug-inuced Liver Injury (DILI):  0.192
AMES Toxicity:  0.274
Rat Oral Acute Toxicity:  0.269
Maximum Recommended Daily Dose:  0.025
Skin Sensitization:  0.218
Carcinogencity:  0.699
Eye Corrosion:  0.005
Eye Irritation:  0.028
Respiratory Toxicity:  0.96

Download Data

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  Natural Product: NPC234132

Natural Product ID:  NPC234132
Common Name*:   LHDWRKICQLTVDL-ROGNWKECSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LHDWRKICQLTVDL-ROGNWKECSA-N
Standard InCHI:  InChI=1S/C15H22O10/c16-3-6-9(19)10(20)11(21)14(23-6)24-13-7-5(1-2-22-13)8(18)12-15(7,4-17)25-12/h1-2,5-14,16-21H,3-4H2/t5-,6-,7-,8+,9-,10+,11-,12+,13+,14+,15-/m0/s1
SMILES:  C1=CO[C@@H]([C@@H]2[C@H]1[C@H]([C@@H]1[C@@]2(CO)O1)O)O[C@@H]1[C@H]([C@@H]([C@H]([C@H](CO)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   53297354
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002207] O-glycosyl compounds

*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
NPO11577 Buddleja officinalis Species Scrophulariaceae Eukaryota flowers bought from a drugstore in Beijing n.a. PMID[10514305]
NPO21324 Plantago major Species Plantaginaceae Eukaryota Whole Plant the surroundings of Uppsala, Sweden 1998-SEP PMID[11421736]
NPO21324 Plantago major Species Plantaginaceae Eukaryota Entire plants the surroundings of Uppsala, Sweden 1998-SEP PMID[11421736]
NPO11577 Buddleja officinalis Species Scrophulariaceae Eukaryota flower buds n.a. n.a. PMID[14738377]
NPO30241 Picrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. root n.a. PMID[15133218]
NPO30241 Picrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. root n.a. PMID[15706916]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota fruits n.a. n.a. PMID[17625893]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota Fruits n.a. n.a. PMID[18293924]
NPO2890 Scrophularia lepidota Species Scrophulariaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota n.a. n.a. n.a. PMID[20192247]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota n.a. fruit n.a. PMID[21319773]
NPO11577 Buddleja officinalis Species Scrophulariaceae Eukaryota flowers n.a. n.a. PMID[21524582]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota fruits n.a. n.a. PMID[22445674]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota Roots n.a. n.a. PMID[22916954]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota fruits n.a. n.a. PMID[23623680]
NPO30241 Picrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[24035096]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. seed n.a. PMID[24895551]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota fruits n.a. n.a. PMID[25735399]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota Fruits n.a. n.a. PMID[28322565]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota stem bark Medicinal Plant Garden, College of Pharmacy, Ewha Womans University 2013-DEC PMID[28787158]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota Fruits n.a. n.a. PMID[28968119]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[9599262]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[9784154]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30241 Picrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12531 Gmelina philippensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17556 Verbascum lychnites Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2890 Scrophularia lepidota Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9035 Verbascum thapsus Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8178 Asystasia intrusa Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5166 Adonis sutchuenensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11577 Buddleja officinalis Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5166 Adonis sutchuenensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17556 Verbascum lychnites Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11577 Buddleja officinalis Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2890 Scrophularia lepidota Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9035 Verbascum thapsus Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12531 Gmelina philippensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8178 Asystasia intrusa Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18120 Radix rehmanniae Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11577 Buddleja officinalis Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30241 Picrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17556 Verbascum lychnites Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11577 Buddleja officinalis Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5166 Adonis sutchuenensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11577 Buddleja officinalis Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22079 Paulownia tomentosa Species Paulowniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2890 Scrophularia lepidota Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9035 Verbascum thapsus Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8178 Asystasia intrusa Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae 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 NPC234132 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 NPC234132 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