Structure

Physi-Chem Properties

Molecular Weight:  302.17
Volume:  289.408
LogP:  -3.745
LogD:  -2.191
LogS:  -1.067
# Rotatable Bonds:  12
TPSA:  197.41
# H-Bond Aceptor:  10
# H-Bond Donor:  10
# Rings:  0
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.13
Synthetic Accessibility Score:  3.027
Fsp3:  0.636
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.854
MDCK Permeability:  0.0010506282560527325
Pgp-inhibitor:  0.001
Pgp-substrate:  0.508
Human Intestinal Absorption (HIA):  0.078
20% Bioavailability (F20%):  0.884
30% Bioavailability (F30%):  0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.344
Plasma Protein Binding (PPB):  7.234793663024902%
Volume Distribution (VD):  0.464
Pgp-substrate:  91.5650863647461%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.013
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.033
CYP2C9-inhibitor:  0.09
CYP2C9-substrate:  0.035
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.174
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.004

ADMET: Excretion

Clearance (CL):  2.019
Half-life (T1/2):  0.611

ADMET: Toxicity

hERG Blockers:  0.048
Human Hepatotoxicity (H-HT):  0.034
Drug-inuced Liver Injury (DILI):  0.008
AMES Toxicity:  0.045
Rat Oral Acute Toxicity:  0.023
Maximum Recommended Daily Dose:  0.011
Skin Sensitization:  0.123
Carcinogencity:  0.052
Eye Corrosion:  0.003
Eye Irritation:  0.016
Respiratory Toxicity:  0.055

Download Data

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

  Natural Product: NPC5178

Natural Product ID:  NPC5178
Common Name*:   PMGDADKJMCOXHX-BQBZGAKWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PMGDADKJMCOXHX-BQBZGAKWSA-N
Standard InCHI:  InChI=1S/C11H22N6O4/c12-6(2-1-5-16-11(14)15)9(19)17-7(10(20)21)3-4-8(13)18/h6-7H,1-5,12H2,(H2,13,18)(H,17,19)(H,20,21)(H4,14,15,16)/t6-,7-/m0/s1
SMILES:  C(C[C@@H](C(=N[C@@H](CCC(=N)O)C(=O)O)O)N)CNC(=N)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   7019985
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:0004830] Dipeptides

*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
NPO997 Peltodon longipes Species Lamiaceae Eukaryota roots Santa Maria, South Brazil 2007-Dec PMID[21775156]
NPO2853 Eschweilera coriacea Species Lecythidaceae Eukaryota bark Suriname rainforest n.a. PMID[9677272]
NPO5665 Ulva pertusa Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5665 Ulva pertusa Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3809 Eucalyptus cladocalyx Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5665 Ulva pertusa Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2853 Eschweilera coriacea Species Lecythidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO997 Peltodon longipes Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5665 Ulva pertusa Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3809 Eucalyptus cladocalyx Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23741 Aspergillus violaceus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1920 Podocarpus elongata Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6621 Salvadora persica Species Salvadoraceae 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 NPC5178 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 NPC5178 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