Structure

Physi-Chem Properties

Molecular Weight:  1092.13
Volume:  979.3
LogP:  2.643
LogD:  1.509
LogS:  -1.655
# Rotatable Bonds:  19
TPSA:  510.94
# H-Bond Aceptor:  30
# H-Bond Donor:  17
# Rings:  7
# Heavy Atoms:  30

MedChem Properties

QED Drug-Likeness Score:  0.034
Synthetic Accessibility Score:  5.155
Fsp3:  0.125
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -7.37
MDCK Permeability:  9.899844371830113e-06
Pgp-inhibitor:  0.339
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.999
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  85.75025177001953%
Volume Distribution (VD):  0.168
Pgp-substrate:  42.517066955566406%

ADMET: Metabolism

CYP1A2-inhibitor:  0.718
CYP1A2-substrate:  0.002
CYP2C19-inhibitor:  0.008
CYP2C19-substrate:  0.007
CYP2C9-inhibitor:  0.149
CYP2C9-substrate:  0.006
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.038
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.001

ADMET: Excretion

Clearance (CL):  15.51
Half-life (T1/2):  0.987

ADMET: Toxicity

hERG Blockers:  0.074
Human Hepatotoxicity (H-HT):  0.199
Drug-inuced Liver Injury (DILI):  0.984
AMES Toxicity:  0.031
Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.003
Skin Sensitization:  0.986
Carcinogencity:  0.004
Eye Corrosion:  0.003
Eye Irritation:  0.968
Respiratory Toxicity:  0.0

Download Data

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

  Natural Product: NPC312727

Natural Product ID:  NPC312727
Common Name*:   ZYDLAYCPLOHXHH-YHNAUUMRSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZYDLAYCPLOHXHH-YHNAUUMRSA-N
Standard InCHI:  InChI=1S/C48H36O30/c49-20-1-14(2-21(50)33(20)60)42(66)72-13-32-39(75-44(68)16-5-24(53)35(62)25(54)6-16)40(76-46(70)19-11-30(59)38(65)31(12-19)73-43(67)15-3-22(51)34(61)23(52)4-15)41(77-45(69)17-7-26(55)36(63)27(56)8-17)48(74-32)78-47(71)18-9-28(57)37(64)29(58)10-18/h1-12,32,39-41,48-65H,13H2/t32-,39-,40+,41-,48+/m1/s1
SMILES:  c1c(cc(c(c1O)O)O)C(=O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)OC(=O)c1cc(c(c(c1)O)O)O)OC(=O)c1cc(c(c(c1)O)O)O)OC(=O)c1cc(c(c(c1)OC(=O)c1cc(c(c(c1)O)O)O)O)O)OC(=O)c1cc(c(c(c1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   16164119
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000238] Tannins
        • [CHEMONTID:0001710] Hydrolyzable tannins

*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
NPO6039 Aglaia laxiflora Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[10785416]
NPO8621 Cylindrospermopsis raciborskii Species Aphanizomenonaceae Bacteria n.a. n.a. n.a. PMID[11223086]
NPO9973 Euphorbia turczaninowii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[11520228]
NPO8621 Cylindrospermopsis raciborskii Species Aphanizomenonaceae Bacteria n.a. n.a. n.a. PMID[14559084]
NPO7381 Ircinia spinosula Species Irciniidae Eukaryota n.a. Bay of Naples, Italy n.a. PMID[7714539]
NPO5065 Cladonia fallax Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9734 Vincetoxicum hirundinaria Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5065 Cladonia fallax Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9207 Styrax ferrugineus Species Styracaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8621 Cylindrospermopsis raciborskii Species Aphanizomenonaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO7013 Dicoma capensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15448 Chrysothamnus parryi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5301 Haplophyllum ferganicum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9973 Euphorbia turczaninowii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4073 Geranium sylvaticum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5541 Crotalaria aegyptiaca Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3924 Penicillium alutaceum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2723 Artemisia carvifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26170 Haliclona mucosa Species Chalinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8773 Sonchus ortunoi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6039 Aglaia laxiflora Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9207 Styrax ferrugineus Species Styracaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9734 Vincetoxicum hirundinaria Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8909 Pteris radiata Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7625 Scopolia hladnikiana Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3119 Cephalaria uralensis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO762 Digitalis isabelliana Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5065 Cladonia fallax Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8437 Encyothalia cliftonii Species Sporochnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7381 Ircinia spinosula Species Irciniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2174 Polysiphonia elongata Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO550 Callicarpa maingayi Species Lamiaceae 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 NPC312727 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 NPC312727 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