Structure

Physi-Chem Properties

Molecular Weight:  213.99
Volume:  178.562
LogP:  -0.097
LogD:  0.461
LogS:  -1.803
# Rotatable Bonds:  1
TPSA:  58.86
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.557
Synthetic Accessibility Score:  4.791
Fsp3:  0.429
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.826
MDCK Permeability:  9.464186405239161e-06
Pgp-inhibitor:  0.002
Pgp-substrate:  0.039
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.023

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.936
Plasma Protein Binding (PPB):  64.35801696777344%
Volume Distribution (VD):  0.582
Pgp-substrate:  10.155847549438477%

ADMET: Metabolism

CYP1A2-inhibitor:  0.215
CYP1A2-substrate:  0.182
CYP2C19-inhibitor:  0.087
CYP2C19-substrate:  0.679
CYP2C9-inhibitor:  0.028
CYP2C9-substrate:  0.268
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.163
CYP3A4-inhibitor:  0.014
CYP3A4-substrate:  0.262

ADMET: Excretion

Clearance (CL):  5.395
Half-life (T1/2):  0.855

ADMET: Toxicity

hERG Blockers:  0.093
Human Hepatotoxicity (H-HT):  0.124
Drug-inuced Liver Injury (DILI):  0.978
AMES Toxicity:  0.529
Rat Oral Acute Toxicity:  0.862
Maximum Recommended Daily Dose:  0.03
Skin Sensitization:  0.893
Carcinogencity:  0.332
Eye Corrosion:  0.081
Eye Irritation:  0.52
Respiratory Toxicity:  0.985

Download Data

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

  Natural Product: NPC314800

Natural Product ID:  NPC314800
Common Name*:   holomycin
IUPAC Name:   n.a.
Synonyms:   Holomycin
Standard InCHIKey:  HBUNPJGMNVQSBX-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H6N2O2S2/c1-3(10)8-5-6-4(2-12-13-6)9-7(5)11/h2H,1H3,(H,8,10)(H,9,11)
SMILES:  CC(=Nc1c(O)nc2c1ssc2)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10262683
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0003282] N-arylamides
          • [CHEMONTID:0004506] N-acetylarylamines

*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
NPO41578 Vibrio coralliilyticus + Photobacterium galatheae Species n.a. n.a. n.a. n.a. n.a. PMID[33693627]

☑ 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
NPT17 Organism Staphylococcus epidermidis Staphylococcus epidermidis MIC = 12.5 ug.mL-1 PMID[486731]
NPT17 Organism Staphylococcus epidermidis Staphylococcus epidermidis MBC = 50.0 ug ml-1 PMID[486731]
NPT17 Organism Staphylococcus epidermidis Staphylococcus epidermidis Ratio = 4.0 n.a. PMID[486731]
NPT2 Others Unspecified IC50 > 100.0 ug.mL-1 PMID[486731]

☑ 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 NPC314800 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
0.6716 Remote Similarity NPC40598
0.6522 Remote Similarity NPC316309
0.6324 Remote Similarity NPC477864
0.625 Remote Similarity NPC477862
0.6164 Remote Similarity NPC477863
0.5818 Remote Similarity NPC145077
0.5763 Remote Similarity NPC282097

  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 NPC314800 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
NPD

  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