Structure

Physi-Chem Properties

Molecular Weight:  286.08
Volume:  285.119
LogP:  3.127
LogD:  2.827
LogS:  -4.037
# Rotatable Bonds:  2
TPSA:  75.99
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.887
Synthetic Accessibility Score:  2.696
Fsp3:  0.188
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.697
MDCK Permeability:  8.2738642959157e-06
Pgp-inhibitor:  0.013
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.928

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.053
Plasma Protein Binding (PPB):  95.35382843017578%
Volume Distribution (VD):  0.675
Pgp-substrate:  3.799860954284668%

ADMET: Metabolism

CYP1A2-inhibitor:  0.95
CYP1A2-substrate:  0.859
CYP2C19-inhibitor:  0.953
CYP2C19-substrate:  0.107
CYP2C9-inhibitor:  0.897
CYP2C9-substrate:  0.954
CYP2D6-inhibitor:  0.822
CYP2D6-substrate:  0.877
CYP3A4-inhibitor:  0.789
CYP3A4-substrate:  0.186

ADMET: Excretion

Clearance (CL):  11.929
Half-life (T1/2):  0.516

ADMET: Toxicity

hERG Blockers:  0.091
Human Hepatotoxicity (H-HT):  0.52
Drug-inuced Liver Injury (DILI):  0.941
AMES Toxicity:  0.717
Rat Oral Acute Toxicity:  0.642
Maximum Recommended Daily Dose:  0.896
Skin Sensitization:  0.713
Carcinogencity:  0.731
Eye Corrosion:  0.005
Eye Irritation:  0.929
Respiratory Toxicity:  0.884

Download Data

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

  Natural Product: NPC75455

Natural Product ID:  NPC75455
Common Name*:   HMUJXQRRKBLVOO-CQSZACIVSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HMUJXQRRKBLVOO-CQSZACIVSA-N
Standard InCHI:  InChI=1S/C16H14O5/c1-20-11-4-2-9(3-5-11)14-8-13(19)16-12(18)6-10(17)7-15(16)21-14/h2-7,14,17-18H,8H2,1H3/t14-/m1/s1
SMILES:  COc1ccc(cc1)[C@H]1CC(=O)c2c(cc(cc2O1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   1149877
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002596] 4'-O-methylated flavonoids

*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
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. PMID[17548953]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota Aerial parts n.a. n.a. PMID[20166702]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. exocarp n.a. PMID[21114277]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota n.a. aerial part n.a. PMID[21171571]
NPO27751 Pinus radiata Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[23131896]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. PMID[24675423]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Enemore, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Gedo, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Holleta, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Bako, Ethiopia PMID[24926420]
NPO3013 Clathria basilana Species Microcionidae Eukaryota n.a. n.a. n.a. PMID[29094598]
NPO17260 Xanthosoma sagittifolium Species Araceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO17260 Xanthosoma sagittifolium Species Araceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO17260 Xanthosoma sagittifolium Species Araceae Eukaryota n.a. n.a. Database[FooDB]
NPO27751 Pinus radiata Species Pinaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28448 Agathis dammara Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19982 Crotalaria sessiliflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28448 Agathis dammara Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28304 Viburnum tinus Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27751 Pinus radiata Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19982 Crotalaria sessiliflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28448 Agathis dammara Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13178 Ornithoglossum viride Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28429 Streptomyces jumonjinensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO13876 Cedrela salvadorensis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27507 Streptomyces ribosidificus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9569 Licaria chrysophylla Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17260 Xanthosoma sagittifolium Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5280 Rubia tetragona Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19982 Crotalaria sessiliflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14369 Pocillopora eydouxi Species Pocilloporidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28448 Agathis dammara Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27845 Lanice conchilega Species Terebellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27461 Odocoileus hemionus Species Cervidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4700 Pertusaria truncata Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28304 Viburnum tinus Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12521 Sphaeranthus confertifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27751 Pinus radiata Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13669 Hertia cheirifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3013 Clathria basilana Species Microcionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27638 Phoenix hanceana Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14470 Polypodium decumanum Species Polypodiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14169 Acrocarpia paniculata Species Sargassaceae 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 NPC75455 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 NPC75455 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