Structure

Physi-Chem Properties

Molecular Weight:  212.07
Volume:  206.365
LogP:  1.644
LogD:  4.107
LogS:  -3.056
# Rotatable Bonds:  4
TPSA:  64.99
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.762
Synthetic Accessibility Score:  1.728
Fsp3:  0.3
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.656
MDCK Permeability:  2.7137177312397398e-05
Pgp-inhibitor:  0.016
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.178

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.8
Plasma Protein Binding (PPB):  77.37140655517578%
Volume Distribution (VD):  0.546
Pgp-substrate:  18.18143081665039%

ADMET: Metabolism

CYP1A2-inhibitor:  0.905
CYP1A2-substrate:  0.955
CYP2C19-inhibitor:  0.191
CYP2C19-substrate:  0.809
CYP2C9-inhibitor:  0.105
CYP2C9-substrate:  0.773
CYP2D6-inhibitor:  0.031
CYP2D6-substrate:  0.734
CYP3A4-inhibitor:  0.059
CYP3A4-substrate:  0.282

ADMET: Excretion

Clearance (CL):  11.062
Half-life (T1/2):  0.931

ADMET: Toxicity

hERG Blockers:  0.03
Human Hepatotoxicity (H-HT):  0.07
Drug-inuced Liver Injury (DILI):  0.246
AMES Toxicity:  0.014
Rat Oral Acute Toxicity:  0.011
Maximum Recommended Daily Dose:  0.033
Skin Sensitization:  0.418
Carcinogencity:  0.024
Eye Corrosion:  0.148
Eye Irritation:  0.96
Respiratory Toxicity:  0.095

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

  Natural Product: NPC277728

Natural Product ID:  NPC277728
Common Name*:   ZMXJAEGJWHJMGX-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZMXJAEGJWHJMGX-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H12O5/c1-13-7-4-6(10(12)15-3)5-8(14-2)9(7)11/h4-5,11H,1-3H3
SMILES:  COc1cc(cc(c1O)OC)C(=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   70164
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0000176] Benzoic acids and derivatives
          • [CHEMONTID:0001248] Hydroxybenzoic acid derivatives
            • [CHEMONTID:0001251] Gallic acid 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
NPO27255 Macaranga alnifolia Species Euphorbiaceae Eukaryota n.a. leaf n.a. DOI[10.1016/0031-9422(92)80315-6]
NPO2073 Ancistrocladus korupensis Species Ancistrocladaceae Eukaryota n.a. Cameroon n.a. PMID[11430019]
NPO27255 Macaranga alnifolia Species Euphorbiaceae Eukaryota n.a. fruit n.a. PMID[17326683]
NPO27255 Macaranga alnifolia Species Euphorbiaceae Eukaryota n.a. Madagascar rainforest n.a. PMID[17326683]
NPO13278 Strychnos spinosa Species Loganiaceae Eukaryota Leaves n.a. n.a. PMID[17637068]
NPO15233 Balanophora japonica Species Balanophoraceae Eukaryota n.a. n.a. n.a. PMID[18302336]
NPO2073 Ancistrocladus korupensis Species Ancistrocladaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO11871 Illicium difengpi Species Schisandraceae Eukaryota stem bark n.a. n.a. PMID[20411974]
NPO26132 Buxus natalensis Species Buxaceae Eukaryota n.a. uMhalanga Rocks nature reserve, Durban, South Africa 2007-FEB PMID[20954721]
NPO26132 Buxus natalensis Species Buxaceae Eukaryota n.a. bark n.a. PMID[20954721]
NPO27700 Alphitonia excelsa Species Rhamnaceae Eukaryota n.a. xylem n.a. PMID[21992235]
NPO5470 Cynoglossum amabile Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[22432912]
NPO4617 Tanacetum cinerariifolium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[24253739]
NPO2330 Alchornea cordifolia Species Euphorbiaceae Eukaryota n.a. root n.a. PMID[26724423]
NPO2330 Alchornea cordifolia Species Euphorbiaceae Eukaryota n.a. stem n.a. PMID[26724423]
NPO27999 Aconitum nagarum Species Ranunculaceae Eukaryota n.a. root n.a. Europe PMC[335013]
NPO2073 Ancistrocladus korupensis Species Ancistrocladaceae Eukaryota n.a. n.a. n.a. PMID[9249970]
NPO2073 Ancistrocladus korupensis Species Ancistrocladaceae Eukaryota n.a. n.a. n.a. PMID[9873424]
NPO15233 Balanophora japonica Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11871 Illicium difengpi Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13278 Strychnos spinosa Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5470 Cynoglossum amabile Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9194 Taraxacum formosanum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15233 Balanophora japonica Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2073 Ancistrocladus korupensis Species Ancistrocladaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23772 Tetradium glabrifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10098 Glycosmis pseudoracemosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13278 Strychnos spinosa Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11302 Hymenidium lindleyanum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4617 Tanacetum cinerariifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4203 Phlomoides rotata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12487 Juniperus horizontalis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9194 Taraxacum formosanum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5470 Cynoglossum amabile Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11871 Illicium difengpi Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5507 Eubotryoides grayana Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5470 Cynoglossum amabile Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11871 Illicium difengpi Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11871 Illicium difengpi Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4203 Phlomoides rotata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14526 Plectranthus caninus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27255 Macaranga alnifolia Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2330 Alchornea cordifolia Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13278 Strychnos spinosa Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13848 Amomum daniellii Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24059 Agathosma recurvifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14947 Lathyrus tingitanus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27615 Ambrosia deltoidea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9194 Taraxacum formosanum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27700 Alphitonia excelsa Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6906 Atalantia wightii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26132 Buxus natalensis Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5398 Peucedanum oroselinum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4617 Tanacetum cinerariifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27999 Aconitum nagarum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7521 Hygrophorus eburneus Species Hygrophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3761 Plectosphaerella cucumerina Species Plectosphaerellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27765 Bryopsis plumosa Species Bryopsidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11430 Inula grantioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18873.2 Salmonella enterica subsp. enterica serovar bovismorbificans Subspecies Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO4203 Phlomoides rotata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5470 Cynoglossum amabile Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23772 Tetradium glabrifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12487 Juniperus horizontalis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1759 Alexandrium excavatum Species Gonyaulacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16801 Cota tinctoria Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15145 Rauvolfia salicifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10098 Glycosmis pseudoracemosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3965 Corynanthe pachyceras Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1109 Corydalis persica Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15329 Rhizoplaca baranowii Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5507 Eubotryoides grayana Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15233 Balanophora japonica Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13647 Calcarisporium thermophilum Species n.a. 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
NPT21912 ORGANISM Hylobius abietis Hylobius abietis AFI = 10.0 % PMID[573979]

☑ 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 NPC277728 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 NPC277728 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