Structure

Physi-Chem Properties

Molecular Weight:  247.2
Volume:  270.044
LogP:  3.667
LogD:  4.039
LogS:  -3.265
# Rotatable Bonds:  3
TPSA:  50.74
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.819
Synthetic Accessibility Score:  4.741
Fsp3:  0.867
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.806
MDCK Permeability:  9.674522516434081e-06
Pgp-inhibitor:  0.037
Pgp-substrate:  0.932
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.464
30% Bioavailability (F30%):  0.023

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.483
Plasma Protein Binding (PPB):  45.917205810546875%
Volume Distribution (VD):  1.355
Pgp-substrate:  37.73134231567383%

ADMET: Metabolism

CYP1A2-inhibitor:  0.357
CYP1A2-substrate:  0.149
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.815
CYP2C9-inhibitor:  0.017
CYP2C9-substrate:  0.084
CYP2D6-inhibitor:  0.113
CYP2D6-substrate:  0.602
CYP3A4-inhibitor:  0.25
CYP3A4-substrate:  0.297

ADMET: Excretion

Clearance (CL):  10.302
Half-life (T1/2):  0.298

ADMET: Toxicity

hERG Blockers:  0.282
Human Hepatotoxicity (H-HT):  0.736
Drug-inuced Liver Injury (DILI):  0.844
AMES Toxicity:  0.019
Rat Oral Acute Toxicity:  0.946
Maximum Recommended Daily Dose:  0.375
Skin Sensitization:  0.731
Carcinogencity:  0.263
Eye Corrosion:  0.008
Eye Irritation:  0.078
Respiratory Toxicity:  0.913

Download Data

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

  Natural Product: NPC57599

Natural Product ID:  NPC57599
Common Name*:   CEMGHQSRVMICPV-RSLMWUCJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CEMGHQSRVMICPV-RSLMWUCJSA-N
Standard InCHI:  InChI=1S/C15H25N3/c1-3-5-9-8-10-6-7-12-13(10)14(11(9)4-2)18-15(16)17-12/h9-10,12-13H,3-8H2,1-2H3,(H3,16,17,18)/t9-,10+,12+,13-/m1/s1
SMILES:  CCC[C@@H]1C[C@@H]2CC[C@H]3[C@@H]2C(=C1CC)NC(=N)N3
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3261945
PubChem CID:   86302287
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0004788] Diazanaphthalenes
        • [CHEMONTID:0004789] Benzodiazines
          • [CHEMONTID:0000485] Quinazolines

*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
NPO21865 Biemna laboutei Species Biemnidae Eukaryota n.a. n.a. n.a. PMID[24601655]
NPO21865 Biemna laboutei Species Biemnidae 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
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 2400.0 nM PMID[479220]

☑ 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 NPC57599 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
0.9359 High Similarity NPC471867
0.6742 Remote Similarity NPC471868
0.6705 Remote Similarity NPC12035
0.6437 Remote Similarity NPC259989
0.6437 Remote Similarity NPC174803
0.6296 Remote Similarity NPC325268
0.6264 Remote Similarity NPC152039
0.6264 Remote Similarity NPC329782
0.6264 Remote Similarity NPC118329
0.6196 Remote Similarity NPC472312
0.6173 Remote Similarity NPC472544
0.617 Remote Similarity NPC24733
0.6087 Remote Similarity NPC474122
0.6044 Remote Similarity NPC211322
0.5977 Remote Similarity NPC21773
0.5957 Remote Similarity NPC171639
0.5851 Remote Similarity NPC283277
0.5843 Remote Similarity NPC476904
0.5795 Remote Similarity NPC265789
0.5789 Remote Similarity NPC161344
0.5778 Remote Similarity NPC125828
0.5773 Remote Similarity NPC56107
0.5714 Remote Similarity NPC7214
0.5682 Remote Similarity NPC472543

  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 NPC57599 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
0.6 Remote Similarity NPD1426 Clinical (unspecified phase)
0.5814 Remote Similarity NPD350 Approved
0.5814 Remote Similarity NPD349 Phase 2
0.5814 Remote Similarity NPD351 Approved
0.5814 Remote Similarity NPD352 Phase 3
0.567 Remote Similarity NPD1353 Suspended
0.5618 Remote Similarity NPD5365 Phase 2

  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