Structure

Physi-Chem Properties

Molecular Weight:  458.23
Volume:  457.899
LogP:  1.34
LogD:  0.8
LogS:  -3.973
# Rotatable Bonds:  3
TPSA:  109.36
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  6
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.597
Synthetic Accessibility Score:  5.449
Fsp3:  0.731
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.478
MDCK Permeability:  1.8243670638184994e-05
Pgp-inhibitor:  0.12
Pgp-substrate:  0.997
Human Intestinal Absorption (HIA):  0.015
20% Bioavailability (F20%):  0.172
30% Bioavailability (F30%):  0.971

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.516
Plasma Protein Binding (PPB):  90.79707336425781%
Volume Distribution (VD):  1.249
Pgp-substrate:  10.849133491516113%

ADMET: Metabolism

CYP1A2-inhibitor:  0.011
CYP1A2-substrate:  0.102
CYP2C19-inhibitor:  0.011
CYP2C19-substrate:  0.607
CYP2C9-inhibitor:  0.034
CYP2C9-substrate:  0.078
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.183
CYP3A4-inhibitor:  0.049
CYP3A4-substrate:  0.357

ADMET: Excretion

Clearance (CL):  5.629
Half-life (T1/2):  0.849

ADMET: Toxicity

hERG Blockers:  0.635
Human Hepatotoxicity (H-HT):  0.911
Drug-inuced Liver Injury (DILI):  0.899
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.972
Maximum Recommended Daily Dose:  0.998
Skin Sensitization:  0.14
Carcinogencity:  0.03
Eye Corrosion:  0.004
Eye Irritation:  0.014
Respiratory Toxicity:  0.958

Download Data

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

  Natural Product: NPC9600

Natural Product ID:  NPC9600
Common Name*:   QMEMRUDWBPMCGJ-NGKLVTAKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QMEMRUDWBPMCGJ-NGKLVTAKSA-N
Standard InCHI:  InChI=1S/C26H34O7/c1-12-14(13-5-6-31-10-13)7-15-20(12)26(4)16(8-19(29)30)25(3)18(28)9-17(27)24(2)11-32-21(22(24)25)23(26)33-15/h5-6,10,14-18,21-23,27-28H,7-9,11H2,1-4H3,(H,29,30)/t14-,15+,16+,17+,18-,21+,22-,23+,24+,25-,26+/m0/s1
SMILES:  CC1=C2[C@@H](C[C@@H]1c1ccoc1)O[C@@H]1[C@H]3[C@H]4[C@](C)(CO3)[C@@H](C[C@@H]([C@]4(C)[C@@H](CC(=O)O)[C@]21C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids
          • [CHEMONTID:0002380] Limonoids

*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
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. bark n.a. PMID[1479382]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota bark n.a. n.a. PMID[1479382]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[1791471]
NPO5587 Chisocheton ceramicus Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[19081726]
NPO5587 Chisocheton ceramicus Species Meliaceae Eukaryota n.a. bark n.a. PMID[21428417]
NPO5587 Chisocheton ceramicus Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[21428417]
NPO5587 Chisocheton ceramicus Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[23395661]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[2614426]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[9322367]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[9917277]
NPO3846 Melia indica Species Meliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26224 Walsura piscidia Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8783 Stachys palustris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3846 Melia indica Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8783 Stachys palustris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8783 Stachys palustris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2423 Melochia corchorifolia Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3846 Melia indica Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO774 Cleome pungens Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7202 Goniothalamus giganteus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1058 Pestalotiopsis heterocornis Species Sporocadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8249 Marcetella moquiniana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26224 Walsura piscidia Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2006 Centaurea sinaica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1594 [enterobacter] aerogenes Species Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO9217 Daphniphyllum angustifolium Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15379 Phalaenopsis schilleriana Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5587 Chisocheton ceramicus Species Meliaceae 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 NPC9600 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 NPC9600 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