Structure

Physi-Chem Properties

Molecular Weight:  484.23
Volume:  481.267
LogP:  3.023
LogD:  1.788
LogS:  -3.999
# Rotatable Bonds:  14
TPSA:  134.66
# H-Bond Aceptor:  10
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.363
Synthetic Accessibility Score:  4.52
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.646
MDCK Permeability:  7.135180931072682e-05
Pgp-inhibitor:  0.823
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.076
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.908
Plasma Protein Binding (PPB):  53.33528137207031%
Volume Distribution (VD):  1.083
Pgp-substrate:  31.24918556213379%

ADMET: Metabolism

CYP1A2-inhibitor:  0.053
CYP1A2-substrate:  0.019
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.084
CYP2C9-inhibitor:  0.081
CYP2C9-substrate:  0.044
CYP2D6-inhibitor:  0.097
CYP2D6-substrate:  0.023
CYP3A4-inhibitor:  0.415
CYP3A4-substrate:  0.259

ADMET: Excretion

Clearance (CL):  3.85
Half-life (T1/2):  0.644

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.516
Drug-inuced Liver Injury (DILI):  0.914
AMES Toxicity:  0.99
Rat Oral Acute Toxicity:  0.081
Maximum Recommended Daily Dose:  0.841
Skin Sensitization:  0.888
Carcinogencity:  0.949
Eye Corrosion:  0.172
Eye Irritation:  0.203
Respiratory Toxicity:  0.915

Download Data

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

  Natural Product: NPC274550

Natural Product ID:  NPC274550
Common Name*:   Hadacidin
IUPAC Name:   2-[formyl(hydroxy)amino]acetic acid
Synonyms:   Hadacidin
Standard InCHIKey:  URJHVPKUWOUENU-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C3H5NO4/c5-2-4(8)1-3(6)7/h2,8H,1H2,(H,6,7)
SMILES:  C(C(=O)O)N(C=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL331373
PubChem CID:   12717
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:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0002965] N-formyl-alpha amino acids and derivatives
                • [CHEMONTID:0002964] N-formyl-alpha amino acids

*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
NPO11443 Bistorta amplexicaulis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO12507 Bixa orellana Species Bixaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14068 Viburnum prunifolium Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18450 Oxytropis campestris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12507 Bixa orellana Species Bixaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21233 Pteris linearis Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14068 Viburnum prunifolium Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14068 Viburnum prunifolium Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15629 Byssochlamys nivea Species Thermoascaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21402 Vespula vulgaris Species Vespidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21233 Pteris linearis Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14471 Streptomyces luridus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6109 Lonchocarpus subglaucescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14365 Eysenhardtia subcoriacea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10938 Psychotria prunifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12032 Oxylobus adscendens n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO10234 [brevibacterium] flavum Species Corynebacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO15947 Penicillium glabrum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18450 Oxytropis campestris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14986 Haplophyton crooksii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11443 Bistorta amplexicaulis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4434 Bignonia hyacinthina Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9544 Eria angustifolia Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13357 Vancouveria hexandra Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14068 Viburnum prunifolium Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5236 Polygonatum biflorum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO390 Tectocoris diophthalmus Species Scutelleridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12507 Bixa orellana Species Bixaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9299.2 Hordeum vulgare subsp. vulgare Subspecies Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10103 Senecio iodanthus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8822 Alphonsea ventricosa Species Annonaceae 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
NPT5640 Individual Protein Adenylosuccinate synthetase 2 Homo sapiens IC50 = 3500.0 nM PMID[548063]
NPT2 Others Unspecified Inhibition = 80.0 % PMID[548065]

☑ 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 NPC274550 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
0.6667 Remote Similarity NPC216443
0.6585 Remote Similarity NPC134570
0.625 Remote Similarity NPC59650
0.5897 Remote Similarity NPC126681
0.5714 Remote Similarity NPC260324

  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 NPC274550 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
0.675 Remote Similarity NPD8800 Approved
0.625 Remote Similarity NPD8796 Approved
0.625 Remote Similarity NPD8795 Approved
0.625 Remote Similarity NPD8799 Approved
0.6222 Remote Similarity NPD335 Approved
0.6222 Remote Similarity NPD331 Approved
0.6087 Remote Similarity NPD334 Phase 3
0.6087 Remote Similarity NPD1433 Approved
0.6087 Remote Similarity NPD1437 Approved
0.5897 Remote Similarity NPD7371 Approved
0.5833 Remote Similarity NPD2260 Approved
0.5833 Remote Similarity NPD2261 Phase 3
0.5778 Remote Similarity NPD333 Approved
0.5778 Remote Similarity NPD330 Approved
0.5778 Remote Similarity NPD336 Approved
0.5778 Remote Similarity NPD332 Approved
0.5652 Remote Similarity NPD1438 Approved
0.5652 Remote Similarity NPD1434 Approved
0.5652 Remote Similarity NPD1435 Approved
0.5652 Remote Similarity NPD1436 Approved

  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