Structure

Physi-Chem Properties

Molecular Weight:  342.19
Volume:  326.121
LogP:  0.277
LogD:  -0.14
LogS:  -0.149
# Rotatable Bonds:  10
TPSA:  91.49
# H-Bond Aceptor:  7
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.453
Synthetic Accessibility Score:  3.503
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.216
MDCK Permeability:  4.524061750998953e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.777
Human Intestinal Absorption (HIA):  0.859
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.04

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.126
Plasma Protein Binding (PPB):  23.256397247314453%
Volume Distribution (VD):  0.943
Pgp-substrate:  70.14987182617188%

ADMET: Metabolism

CYP1A2-inhibitor:  0.039
CYP1A2-substrate:  0.144
CYP2C19-inhibitor:  0.06
CYP2C19-substrate:  0.919
CYP2C9-inhibitor:  0.02
CYP2C9-substrate:  0.076
CYP2D6-inhibitor:  0.022
CYP2D6-substrate:  0.899
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.522

ADMET: Excretion

Clearance (CL):  1.583
Half-life (T1/2):  0.727

ADMET: Toxicity

hERG Blockers:  0.064
Human Hepatotoxicity (H-HT):  0.007
Drug-inuced Liver Injury (DILI):  0.114
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.204
Maximum Recommended Daily Dose:  0.021
Skin Sensitization:  0.553
Carcinogencity:  0.064
Eye Corrosion:  0.007
Eye Irritation:  0.242
Respiratory Toxicity:  0.975

Download Data

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

  Natural Product: NPC484493

Natural Product ID:  NPC484493
Common Name*:   IOIMDJXKIMCMIG-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  IOIMDJXKIMCMIG-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H32N4O3P2/c1-9(2)13-20(17,14-10(3)4)19-21(18,15-11(5)6)16-12(7)8/h9-12H,1-8H3,(H2,13,14,17)(H2,15,16,18)
SMILES:  CC(C)NP(=O)(NC(C)C)OP(=O)(NC(C)C)NC(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5420
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000402] Organic phosphoric acids and derivatives
        • [CHEMONTID:0001204] Organic phosphoramides

*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
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[10479323]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[12350167]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[14640527]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota Axinella verrucosa Mediterranean n.a. PMID[14738391]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15043411]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. Sussex Inlet, New South Wales, Australia n.a. PMID[15104517]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15332862]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. Berkeley Pit lake n.a. PMID[17970594]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. New Zealand n.a. PMID[19323568]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19326880]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[20452770]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21126094]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. North Sea n.a. PMID[21126094]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. Limonium tubiflorum n.a. PMID[21146414]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21916432]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22148349]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22458669]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23360521]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23477451]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23603293]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23972215]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24033077]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24437979]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[31433188]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[9392888]
NPO30770 Penicillium sp. Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[Article]

☑ 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
NPT204 Individual Protein Acetylcholinesterase Homo sapiens IC50 = 340000.0 nM PMID[16570913]
NPT439 Individual Protein Butyrylcholinesterase Homo sapiens IC50 = 980.0 nM PMID[16570913]
NPT439 Individual Protein Butyrylcholinesterase Homo sapiens IC50 = 733.0 nM PMID[18817366]
NPT66 Individual Protein Acetylcholinesterase Electrophorus electricus IC50 = 2500.0 nM PMID[18817366]
NPT66 Individual Protein Acetylcholinesterase Electrophorus electricus Inhibition = 1.3 % PMID[31433188]
NPT66 Individual Protein Acetylcholinesterase Electrophorus electricus IC50 > 100000.0 nM PMID[31433188]
NPT3768 Others Cholinesterases; ACHE & BCHE Homo sapiens Ratio IC50 = 350.0 n.a. PMID[16570913]
NPT2 Others Unspecified Ratio IC50 = 3.41 n.a. PMID[18817366]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 10000.0 nM PMID[19734910]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 12589.25 nM PMID[19734910]
NPT67 Individual Protein Cholinesterase Equus caballus Inhibition = 15.1 % PMID[31433188]

☑ 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 NPC484493 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 NPC484493 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