Structure

Physi-Chem Properties

Molecular Weight:  310.05
Volume:  291.456
LogP:  3.947
LogD:  3.33
LogS:  -7.032
# Rotatable Bonds:  1
TPSA:  71.04
# H-Bond Aceptor:  6
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.502
Synthetic Accessibility Score:  2.461
Fsp3:  0.118
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.862
MDCK Permeability:  7.533122698077932e-05
Pgp-inhibitor:  0.728
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.908

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.016
Plasma Protein Binding (PPB):  83.44464874267578%
Volume Distribution (VD):  0.768
Pgp-substrate:  12.171405792236328%

ADMET: Metabolism

CYP1A2-inhibitor:  0.985
CYP1A2-substrate:  0.711
CYP2C19-inhibitor:  0.956
CYP2C19-substrate:  0.177
CYP2C9-inhibitor:  0.751
CYP2C9-substrate:  0.94
CYP2D6-inhibitor:  0.753
CYP2D6-substrate:  0.927
CYP3A4-inhibitor:  0.855
CYP3A4-substrate:  0.116

ADMET: Excretion

Clearance (CL):  11.165
Half-life (T1/2):  0.172

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.947
Drug-inuced Liver Injury (DILI):  0.98
AMES Toxicity:  0.348
Rat Oral Acute Toxicity:  0.11
Maximum Recommended Daily Dose:  0.908
Skin Sensitization:  0.49
Carcinogencity:  0.942
Eye Corrosion:  0.008
Eye Irritation:  0.323
Respiratory Toxicity:  0.324

Download Data

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

  Natural Product: NPC62074

Natural Product ID:  NPC62074
Common Name*:   ZIZYKBRERUNPAU-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZIZYKBRERUNPAU-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C17H10O6/c1-19-8-2-3-9-11(4-8)23-17(18)15-10-5-13-14(21-7-20-13)6-12(10)22-16(9)15/h2-6H,7H2,1H3
SMILES:  COc1ccc2c(c1)oc(=O)c1c3cc4c(cc3oc21)OCO4
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11088179
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0000354] Coumestans

*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
NPO27553 Derris scandens Species Fabaceae Eukaryota n.a. stem n.a. DOI[10.1016/S0031-9422(99)00103-X]
NPO27553 Derris scandens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19969457]
NPO5885 Bathymodiolus thermophilus Species Mytilidae Eukaryota n.a. gill n.a. PMID[21222464]
NPO27553 Derris scandens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21314138]
NPO27553 Derris scandens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25628 Abrus pulchellus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9721 Radix moghaniae philippinensis Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27553 Derris scandens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27553 Derris scandens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25422 Artemisia dracunculoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25708 Erioderma phaeorhizum Species Pannariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24229 Schoenus nigricans Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25052 Diphysa robinioides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25533 Stellaster equestris Species Goniasteridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25730 Prorhinotermes simplex Species Termitoidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25149 Centaurea arguta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5885 Bathymodiolus thermophilus Species Mytilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24691 Astragalus orbiculatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25628 Abrus pulchellus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25758 Aspergillus amstelodami Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24128 Cassinia longifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21669 Acacia sieberana Species Fabaceae 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 NPC62074 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 NPC62074 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