Structure

Physi-Chem Properties

Molecular Weight:  277.17
Volume:  283.161
LogP:  0.663
LogD:  0.249
LogS:  -1.502
# Rotatable Bonds:  0
TPSA:  60.77
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.647
Synthetic Accessibility Score:  6.193
Fsp3:  0.812
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:  -4.666
MDCK Permeability:  1.689699274720624e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.008
Human Intestinal Absorption (HIA):  0.728
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.015

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.819
Plasma Protein Binding (PPB):  11.6592435836792%
Volume Distribution (VD):  1.575
Pgp-substrate:  85.3194580078125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.016
CYP1A2-substrate:  0.224
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.858
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.29
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.631
CYP3A4-inhibitor:  0.075
CYP3A4-substrate:  0.638

ADMET: Excretion

Clearance (CL):  12.234
Half-life (T1/2):  0.302

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.184
Drug-inuced Liver Injury (DILI):  0.031
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.963
Maximum Recommended Daily Dose:  0.924
Skin Sensitization:  0.03
Carcinogencity:  0.943
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.8

Download Data

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

  Natural Product: NPC470666

Natural Product ID:  NPC470666
Common Name*:   Elaiomycin H
IUPAC Name:   n.a.
Synonyms:   Elaiomycin H
Standard InCHIKey:  AEGYQCQXUUGBRT-ICFTUWFRSA-N
Standard InCHI:  InChI=1S/C12H25N3O3/c1-3-4-5-6-7-8-9-15(17)14-11(10-18-2)12(13)16/h11H,3-10H2,1-2H3,(H2,13,16)/b15-14-/t11-/m0/s1
SMILES:  CCCCCCCC/N(=N/[C@H](C(=N)O)COC)/O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2152473
PubChem CID:   n.a.
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

*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
NPO32477 Streptomyces sp. Under-species n.a. n.a. n.a. n.a. n.a. PMID[23013356]

☑ 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
NPT737 Cell Line HUVEC Homo sapiens GI50 = 38.2 ug.mL-1 PMID[528306]
NPT111 Cell Line K562 Homo sapiens GI50 = 37.5 ug.mL-1 PMID[528306]
NPT165 Cell Line HeLa Homo sapiens CC50 = 40.5 ug.mL-1 PMID[528306]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 1150.0 nM PMID[528306]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 4650.0 nM PMID[528306]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 1200.0 nM PMID[528306]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 8570.0 nM PMID[528306]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 3740.0 nM PMID[528306]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 3950.0 nM PMID[528306]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 9840.0 nM PMID[528306]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 5420.0 nM PMID[528306]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 8010.0 nM PMID[528306]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 5990.0 nM PMID[528306]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 9490.0 nM PMID[528306]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 8880.0 nM PMID[528306]
NPT79 Organism Bacillus subtilis Bacillus subtilis IZ = 0.0 mm PMID[528306]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 0.0 mm PMID[528306]
NPT19 Organism Escherichia coli Escherichia coli IZ = 0.0 mm PMID[528306]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa IZ = 0.0 mm PMID[528306]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis IZ = 0.0 mm PMID[528306]
NPT3473 Organism Mycobacterium vaccae Mycobacterium vaccae IZ = 12.0 mm PMID[528306]
NPT3474 Organism Sporidiobolus salmonicolor Sporidiobolus salmonicolor IZ = 14.0 mm PMID[528306]
NPT20 Organism Candida albicans Candida albicans IZ = 0.0 mm PMID[528306]
NPT2242 Organism Penicillium chrysogenum Penicillium chrysogenum IZ = 0.0 mm PMID[528306]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus IZ = 13.0 mm PMID[528306]
NPT21 Organism Aspergillus niger Aspergillus niger IZ = 0.0 mm PMID[528306]
NPT184 Organism Aspergillus terreus Aspergillus terreus IZ = 15.0 mm PMID[528306]

☑ 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 NPC470666 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
0.8148 Intermediate Similarity NPC470664
0.6984 Remote Similarity NPC470665
0.623 Remote Similarity NPC270041
0.6212 Remote Similarity NPC51166
0.6066 Remote Similarity NPC123814
0.6066 Remote Similarity NPC474322
0.6 Remote Similarity NPC105488
0.5932 Remote Similarity NPC96966
0.5932 Remote Similarity NPC121062
0.5932 Remote Similarity NPC29222
0.5806 Remote Similarity NPC137327
0.5775 Remote Similarity NPC470663
0.5763 Remote Similarity NPC289484
0.5763 Remote Similarity NPC319709
0.5735 Remote Similarity NPC17455
0.5735 Remote Similarity NPC145627
0.5692 Remote Similarity NPC8979
0.5625 Remote Similarity NPC471917

  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 NPC470666 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
0.6066 Remote Similarity NPD3215 Phase 1
0.6 Remote Similarity NPD8198 Approved
0.6 Remote Similarity NPD8197 Approved
0.5862 Remote Similarity NPD1152 Phase 2
0.5763 Remote Similarity NPD379 Clinical (unspecified phase)
0.5763 Remote Similarity NPD3211 Approved
0.5738 Remote Similarity NPD3214 Discontinued
0.5676 Remote Similarity NPD3187 Discontinued
0.5667 Remote Similarity NPD362 Phase 1

  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