Structure

Physi-Chem Properties

Molecular Weight:  224.19
Volume:  244.439
LogP:  3.158
LogD:  3.354
LogS:  -3.769
# Rotatable Bonds:  4
TPSA:  41.13
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.744
Synthetic Accessibility Score:  1.83
Fsp3:  0.923
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:  -4.848
MDCK Permeability:  6.277555075939745e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.982
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.072

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.99
Plasma Protein Binding (PPB):  88.36878967285156%
Volume Distribution (VD):  0.798
Pgp-substrate:  8.405144691467285%

ADMET: Metabolism

CYP1A2-inhibitor:  0.462
CYP1A2-substrate:  0.264
CYP2C19-inhibitor:  0.723
CYP2C19-substrate:  0.284
CYP2C9-inhibitor:  0.417
CYP2C9-substrate:  0.906
CYP2D6-inhibitor:  0.085
CYP2D6-substrate:  0.414
CYP3A4-inhibitor:  0.467
CYP3A4-substrate:  0.116

ADMET: Excretion

Clearance (CL):  4.217
Half-life (T1/2):  0.213

ADMET: Toxicity

hERG Blockers:  0.036
Human Hepatotoxicity (H-HT):  0.35
Drug-inuced Liver Injury (DILI):  0.071
AMES Toxicity:  0.012
Rat Oral Acute Toxicity:  0.042
Maximum Recommended Daily Dose:  0.128
Skin Sensitization:  0.592
Carcinogencity:  0.059
Eye Corrosion:  0.003
Eye Irritation:  0.158
Respiratory Toxicity:  0.296

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

  Natural Product: NPC110136

Natural Product ID:  NPC110136
Common Name*:   1,3-Dicyclohexylurea
IUPAC Name:   1,3-dicyclohexylurea
Synonyms:  
Standard InCHIKey:  ADFXKUOMJKEIND-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C13H24N2O/c16-13(14-11-7-3-1-4-8-11)15-12-9-5-2-6-10-12/h11-12H,1-10H2,(H2,14,15,16)
SMILES:  OC(=NC1CCCCC1)NC1CCCCC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1458
PubChem CID:   4277
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000364] Organic carbonic acids and derivatives
        • [CHEMONTID:0000517] Ureas

*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
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. PMID[26562741]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. PMID[29517238]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. PMID[31625751]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. Along the Valencian coast, Spain 2020-Jun&Jul PMID[35161358]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota Herb n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]

☑ 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
NPT48 Individual Protein Lysine-specific demethylase 4D-like Homo sapiens Potency = 35481.3 nM PMID[530446]
NPT531 Individual Protein Nuclear receptor ROR-gamma Mus musculus Potency = 631.0 nM PMID[530446]
NPT109 Individual Protein Cytochrome P450 3A4 Homo sapiens Potency = 3162.3 nM PMID[530446]
NPT4274 Individual Protein Epoxide hydrolase 1 Homo sapiens IC50 = 160.0 nM PMID[530448]
NPT4275 Individual Protein Epoxide hydrolase 1 Mus musculus IC50 = 90.0 nM PMID[530451]
NPT4274 Individual Protein Epoxide hydrolase 1 Homo sapiens IC50 = 160.0 nM PMID[530451]
NPT862 Individual Protein Epoxide hydratase Homo sapiens IC50 = 52.0 nM PMID[530445]
NPT94 Individual Protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 44668.4 nM PMID[530446]
NPT533 Protein-Protein Interaction Runt-related transcription factor 1/Core-binding factor subunit beta Homo sapiens Potency n.a. 50118.7 nM PMID[530446]
NPT862 Individual Protein Epoxide hydratase Homo sapiens IC50 = 52.0 nM PMID[530447]
NPT862 Individual Protein Epoxide hydratase Homo sapiens IC50 = 25.3 nM PMID[530449]
NPT862 Individual Protein Epoxide hydratase Homo sapiens IC50 = 3.0 nM PMID[530450]
NPT35 Others n.a. Solubility = 5000.0 nM PMID[530450]
NPT626 Tissue Liver microsome Homo sapiens Stability = 100.0 % PMID[530450]
NPT626 Tissue Liver microsome Homo sapiens Stability = 22.0 % PMID[530450]
NPT862 Individual Protein Epoxide hydratase Homo sapiens IC50 = 5.1 nM PMID[530450]
NPT2 Others Unspecified Potency n.a. 1584.9 nM PMID[530446]
NPT862 Individual Protein Epoxide hydratase Homo sapiens IC50 = 25.0 nM PMID[530452]
NPT862 Individual Protein Epoxide hydratase Homo sapiens IC50 = 90.0 nM PMID[530453]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 14.36 % PMID[530454]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = -0.19 % PMID[530455]

☑ 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 NPC110136 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
0.62 Remote Similarity NPC270319
0.5962 Remote Similarity NPC321202
0.5849 Remote Similarity NPC319114
0.5769 Remote Similarity NPC240230
0.5769 Remote Similarity NPC167301
0.5714 Remote Similarity NPC324539
0.5692 Remote Similarity NPC118429
0.5672 Remote Similarity NPC278881
0.5625 Remote Similarity NPC320889
0.5625 Remote Similarity NPC476537
0.5625 Remote Similarity NPC216415
0.56 Remote Similarity NPC163099
0.56 Remote Similarity NPC14922

  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 NPC110136 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
0.6491 Remote Similarity NPD9651 Approved
0.6346 Remote Similarity NPD9458 Approved
0.629 Remote Similarity NPD1155 Discontinued
0.6087 Remote Similarity NPD5382 Phase 2
0.6 Remote Similarity NPD3155 Clinical (unspecified phase)
0.6 Remote Similarity NPD321 Phase 3
0.5849 Remote Similarity NPD9227 Discontinued
0.5818 Remote Similarity NPD9241 Approved
0.5797 Remote Similarity NPD3213 Discontinued
0.5741 Remote Similarity NPD390 Approved
0.5741 Remote Similarity NPD718 Approved
0.5692 Remote Similarity NPD9014 Approved
0.5692 Remote Similarity NPD360 Phase 3
0.569 Remote Similarity NPD395 Approved
0.569 Remote Similarity NPD396 Approved
0.5652 Remote Similarity NPD9451 Clinical (unspecified phase)
0.5634 Remote Similarity NPD5386 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