Structure

Physi-Chem Properties

Molecular Weight:  836.45
Volume:  844.192
LogP:  0.006
LogD:  0.403
LogS:  -3.849
# Rotatable Bonds:  16
TPSA:  300.76
# H-Bond Aceptor:  19
# H-Bond Donor:  12
# Rings:  3
# Heavy Atoms:  19

MedChem Properties

QED Drug-Likeness Score:  0.077
Synthetic Accessibility Score:  5.441
Fsp3:  0.512
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.852
MDCK Permeability:  4.745176283904584e-06
Pgp-inhibitor:  0.007
Pgp-substrate:  1.0
Human Intestinal Absorption (HIA):  0.954
20% Bioavailability (F20%):  0.992
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.045
Plasma Protein Binding (PPB):  52.467098236083984%
Volume Distribution (VD):  0.334
Pgp-substrate:  46.9720458984375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.004
CYP2C19-inhibitor:  0.077
CYP2C19-substrate:  0.031
CYP2C9-inhibitor:  0.226
CYP2C9-substrate:  0.371
CYP2D6-inhibitor:  0.078
CYP2D6-substrate:  0.151
CYP3A4-inhibitor:  0.041
CYP3A4-substrate:  0.003

ADMET: Excretion

Clearance (CL):  1.785
Half-life (T1/2):  0.857

ADMET: Toxicity

hERG Blockers:  0.019
Human Hepatotoxicity (H-HT):  0.958
Drug-inuced Liver Injury (DILI):  0.925
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.182
Maximum Recommended Daily Dose:  0.926
Skin Sensitization:  0.21
Carcinogencity:  0.024
Eye Corrosion:  0.003
Eye Irritation:  0.004
Respiratory Toxicity:  0.676

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

  Natural Product: NPC106384

Natural Product ID:  NPC106384
Common Name*:   ZDOVFDLIJJGVQM-VJLBXGKTSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZDOVFDLIJJGVQM-VJLBXGKTSA-N
Standard InCHI:  InChI=1S/C41H60N10O9/c1-24(2)33-37(56)46-30(20-17-26-15-18-28(52)19-16-26)38(57)51(4)25(3)34(53)47-32(23-27-11-6-5-7-12-27)35(54)44-21-9-8-13-29(36(55)50-33)48-41(60)49-31(39(58)59)14-10-22-45-40(42)43/h5-7,11-12,15-16,18-19,24-25,29-33,52H,8-10,13-14,17,20-23H2,1-4H3,(H,44,54)(H,46,56)(H,47,53)(H,50,55)(H,58,59)(H4,42,43,45)(H2,48,49,60)/t25-,29+,30+,31-,32-,33-/m0/s1
SMILES:  CC(C)[C@H]1C(=N[C@H](CCc2ccc(cc2)O)C(=O)N(C)[C@@H](C)C(=N[C@@H](Cc2ccccc2)C(=NCCCC[C@H](C(=N1)O)N=C(N[C@@H](CCCNC(=N)N)C(=O)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:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000348] Peptides
            • [CHEMONTID:0001995] Cyclic peptides

*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
NPO15753 Pterocarpus angolensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11854 Romalea microptera Species Romaleidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4232 Rabdosia coetsoides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16841 Elsholtzia bodinieri Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4232 Rabdosia coetsoides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12128 Ipomoea purpurea Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15753 Pterocarpus angolensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19977 Desmanthus illinoensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12128 Ipomoea purpurea Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15508 Ambrosia cordifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12412 Ormosia cinerea Species Limoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1443 Monomorium fieldi Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19977 Desmanthus illinoensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO911 Sistotrema raduloides Species Corticiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16841 Elsholtzia bodinieri Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14714 Equisetum silvaticum Species Equisetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15753 Pterocarpus angolensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16276 Croton hieronymi Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12128 Ipomoea purpurea Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9159 Narcissus serotinus Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4232 Rabdosia coetsoides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11854 Romalea microptera Species Romaleidae 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 NPC106384 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 NPC106384 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