Structure

Physi-Chem Properties

Molecular Weight:  1081.67
Volume:  1118.715
LogP:  2.942
LogD:  0.826
LogS:  -3.666
# Rotatable Bonds:  15
TPSA:  337.85
# H-Bond Aceptor:  20
# H-Bond Donor:  13
# Rings:  2
# Heavy Atoms:  20

MedChem Properties

QED Drug-Likeness Score:  0.033
Synthetic Accessibility Score:  7.919
Fsp3:  0.75
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.274
MDCK Permeability:  9.524240158498287e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  1.0
Human Intestinal Absorption (HIA):  0.908
20% Bioavailability (F20%):  0.978
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.106
Plasma Protein Binding (PPB):  48.21802520751953%
Volume Distribution (VD):  0.395
Pgp-substrate:  4.750631809234619%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.009
CYP2C19-inhibitor:  0.003
CYP2C19-substrate:  0.119
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.861
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.059
CYP3A4-inhibitor:  0.168
CYP3A4-substrate:  0.096

ADMET: Excretion

Clearance (CL):  1.494
Half-life (T1/2):  0.929

ADMET: Toxicity

hERG Blockers:  0.311
Human Hepatotoxicity (H-HT):  0.981
Drug-inuced Liver Injury (DILI):  0.159
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.067
Maximum Recommended Daily Dose:  1.0
Skin Sensitization:  0.885
Carcinogencity:  0.035
Eye Corrosion:  0.003
Eye Irritation:  0.007
Respiratory Toxicity:  0.913

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

  Natural Product: NPC7130

Natural Product ID:  NPC7130
Common Name*:   QZHGHZHNPQLENX-NFSOQZLOSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QZHGHZHNPQLENX-NFSOQZLOSA-N
Standard InCHI:  InChI=1S/C56H95N3O17/c1-34-18-14-15-22-51(70)75-53(37(4)19-13-11-9-10-12-16-25-59-55(57-7)58-8)38(5)21-17-20-35(2)45(63)28-41(61)26-40(60)27-42(74-52(71)32-50(68)69)29-43-30-48(66)54(72)56(73,76-43)33-49(67)36(3)23-24-44(62)39(6)47(65)31-46(34)64/h9-10,14-15,17-18,20-22,34,36-49,53-54,60-67,72-73H,11-13,16,19,23-33H2,1-8H3,(H,68,69)(H2,57,58,59)/b10-9+,18-14+,21-17+,22-15+,35-20+/t34-,36+,37-,38-,39+,40-,41+,42+,43-,44-,45+,46-,47+,48-,49+,53-,54-,56+/m0/s1
SMILES:  C[C@H]1/C=C/C=C/C(=O)O[C@@H]([C@@H](C)CCC/C=C/CCCNC(=NC)NC)[C@@H](C)/C=C/C=C(C)/[C@@H](C[C@@H](C[C@@H](C[C@H](C[C@H]2C[C@@H]([C@@H]([C@](C[C@H]([C@H](C)CC[C@@H]([C@@H](C)[C@@H](C[C@@H]1O)O)O)O)(O)O2)O)O)OC(=O)CC(=O)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000147] Macrolides and analogues

*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
NPO26420 Swertia perennis Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[1002/hlca.19760590517]
NPO26420 Swertia perennis Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[931752]
NPO25885 Drupella fragum Species Muricidae Eukaryota n.a. n.a. n.a. PMID[9722496]
NPO25782 Crotalaria trifoliastrum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[9784166]
NPO26911 Mesua thwaitesii Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25912 Leontice smirnowii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26420 Swertia perennis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26769 Montanoa tomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26911 Mesua thwaitesii Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26420 Swertia perennis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25912 Leontice smirnowii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26420 Swertia perennis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26616 Piper novae-hollandiae Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26420 Swertia perennis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28906 Cossus cossus Species Cossidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3732 Entoleuca mammata Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4085 Cephalaria lycica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26891 Pinus nigra Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25861 Helminthosporium catenarium Species Massarinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26310 Panax ricinifolius Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27039 Poterium polygamum Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26198 Halimeda scabra Species Halimedaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26998 Goniotrichum elegans n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO25885 Drupella fragum Species Muricidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26911 Mesua thwaitesii Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13835 Aristolochia serpentaria Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26796 Tropaeolum peregrinum Species Tropaeolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11483 Adenocarpus decorticans Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19417 Cochliobolus pallescens Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26769 Montanoa tomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26276 Haplopappus taeda Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25782 Crotalaria trifoliastrum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25912 Leontice smirnowii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26713 Lasius umbratus Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26600 Glottiphyllum longum Species Aizoaceae 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 NPC7130 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 NPC7130 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