Natural Product: NPC300325

Natural Product IDNPC300325
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Carbamic Acid
IUPAC Name azaniumylformate
Synonyms Carbamic Acid
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL125278
PubChem CID 57418154
277
18358786
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000364] Organic carbonic acids and derivatives

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey KXDHJXZQYSOELW-UHFFFAOYSA-N
Standard InCHI InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)
SMILES C(=O)(N)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   61.02 Volume:   51.793
?
Van der Waals volume.
Dense:   1.178 LogP:   -0.795
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.36
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.032
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   1.0
TPSA:   63.32
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   3.0 Rings:   0.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.401 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.083 Fsp3:   0.0
MCE-18:   0.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.003 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.025
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.998 Promiscuous compounds:   0.162

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.6 MDCK Permeability:   -4.46
Pgp-inhibitor:   0.0 Pgp-substrate:   0.441
PAMPA:   0.956
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.008
20% Bioavailability (F20%):   0.031 30% Bioavailability (F30%):   0.027
50% Bioavailability (F50%):   0.082

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.45 MRP1:   0.901
Plasma Protein Binding (PPB):   -0.836% Volume Distribution (VD):   -0.221
Fu: 98.448%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.409
OATP1B3 inhibitor:   0.846 BCRP inhibitor:   0.003
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.159 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.004 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.007
HLM stability:   0.001
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  0.885 Half-life (T1/2):  2.696

ADMET: Toxicity

hERG Blockers:  0.037 hERG Blockers (10um):  0.137
Human Hepatotoxicity (H-HT):  0.463 Drug-induced Liver Injury (DILI):  0.637
AMES Toxicity:  0.369 Rat Oral Acute Toxicity:  0.449
Maximum Recommended Daily Dose:  0.067 Skin Sensitization:  0.492
Carcinogencity:  0.629 Eye Corrosion:  0.534
Eye Irritation:  0.989 Respiratory Toxicity:  0.557
Drug-induced Neurotoxicity:  0.757 Ototoxicity:  0.255
Hematotoxicity:  0.294 Drug-induced Nephrotoxicity:  0.226
Genotoxicity:  0.95 RPMI-8226 Immunitoxicity:  0.024
A549 Cytotoxicity:  0.003 Hek293 Cytotoxicity:  0.012
BCF:   0.126
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   1.688
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   2.852
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   1.975
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[10.1016/0006-291X(79)91731-5]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[10.1093/emboj/18.8.2021]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1091286]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[10977898]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1100617]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[11745165]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[11750815]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12369847]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12467448]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12805358]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. ChEBI[131529]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[13610867]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[13831814]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[14973046]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15031653]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15292242]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15610037]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1644759]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[16630633]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[170247]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[17765195]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[179975]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19026742]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19514719]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19561621]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. PMID[19919095]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[21437340]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[21988831]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22289691]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22855027]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota flower buds and leaves Khon Kaen province, Thailand 2010 PMID[23270663]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23537328]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Leaves n.a. n.a. PMID[23642481]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23676670]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[241475]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24206068]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24783849]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24831709]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24939187]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24966042]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24967680]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[2543976]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[25867074]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26195826]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26337258]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Flowers n.a. n.a. PMID[26462418]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26670289]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26826371]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[29897754]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[30302998]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[318639]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[3283102]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[398096]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4877125]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4879561]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4908789]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[5332408]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6102982]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6284709]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6338507]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[7042909]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[7601837]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[8852895]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[9470222]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[https://doi.org/10.1016/j.jbiosc.2016.12.008]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria 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 Organism Name 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

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT204 Individual protein Acetylcholinesterase Homo sapiens IC50 = 67000.0 nM PMID[10508425]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference
- Homo sapiens DNEL systemic = 7.4 mg/m3 ToxVal

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC300325 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.7143 Intermediate Similarity NPC159900
0.7143 Intermediate Similarity NPC606409
0.625 Remote Similarity NPC301950
0.5556 Remote Similarity NPC68873
0.5556 Remote Similarity NPC323500

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC300325 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.625 Remote Similarity NPD7352 Pre-clinical
0.625 Remote Similarity NPD9749 Approved
0.5556 Remote Similarity NPD7364 Phase 4
0.5556 Remote Similarity NPD9746 Phase 4
0.5556 Remote Similarity NPD9748 Phase 4

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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