Structure

Physi-Chem Properties

Molecular Weight:  478.26
Volume:  489.722
LogP:  2.267
LogD:  2.268
LogS:  -3.615
# Rotatable Bonds:  6
TPSA:  119.36
# H-Bond Aceptor:  8
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.361
Synthetic Accessibility Score:  5.593
Fsp3:  0.731
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:  -5.096
MDCK Permeability:  0.00010427475353935733
Pgp-inhibitor:  0.987
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.872
20% Bioavailability (F20%):  0.008
30% Bioavailability (F30%):  0.86

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.09
Plasma Protein Binding (PPB):  69.30548095703125%
Volume Distribution (VD):  1.481
Pgp-substrate:  26.80199432373047%

ADMET: Metabolism

CYP1A2-inhibitor:  0.021
CYP1A2-substrate:  0.037
CYP2C19-inhibitor:  0.012
CYP2C19-substrate:  0.199
CYP2C9-inhibitor:  0.03
CYP2C9-substrate:  0.063
CYP2D6-inhibitor:  0.189
CYP2D6-substrate:  0.095
CYP3A4-inhibitor:  0.279
CYP3A4-substrate:  0.32

ADMET: Excretion

Clearance (CL):  3.737
Half-life (T1/2):  0.056

ADMET: Toxicity

hERG Blockers:  0.033
Human Hepatotoxicity (H-HT):  0.948
Drug-inuced Liver Injury (DILI):  0.889
AMES Toxicity:  0.025
Rat Oral Acute Toxicity:  0.576
Maximum Recommended Daily Dose:  0.959
Skin Sensitization:  0.088
Carcinogencity:  0.102
Eye Corrosion:  0.008
Eye Irritation:  0.015
Respiratory Toxicity:  0.969

Download Data

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

  Natural Product: NPC470663

Natural Product ID:  NPC470663
Common Name*:   Elaiomycin E
IUPAC Name:   n.a.
Synonyms:   Elaiomycin E
Standard InCHIKey:  GCPVNKGMEZZCJD-UNBCWUHVSA-N
Standard InCHI:  InChI=1S/C13H26N2O4/c1-4-5-6-7-12(17)8-9-15(18)14-13(10-19-3)11(2)16/h8-9,11-13,16-17H,4-7,10H2,1-3H3/b9-8+,15-14-/t11-,12?,13-/m0/s1
SMILES:  CCCCCC(/C=C/N(=N/[C@H]([C@@H](O)C)COC)/O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2152470
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0003630] Organic 1,3-dipolar compounds
      • [CHEMONTID:0003631] Allyl-type 1,3-dipolar organic compounds
        • [CHEMONTID:0002037] Azoxy compounds

*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 = 31.2 ug.mL-1 PMID[450170]
NPT111 Cell Line K562 Homo sapiens GI50 = 30.3 ug.mL-1 PMID[450170]
NPT165 Cell Line HeLa Homo sapiens CC50 > 50.0 ug.mL-1 PMID[450170]
NPT79 Organism Bacillus subtilis Bacillus subtilis IZ = 10.0 mm PMID[450170]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 0.0 mm PMID[450170]
NPT19 Organism Escherichia coli Escherichia coli IZ = 0.0 mm PMID[450170]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa IZ = 10.0 mm PMID[450170]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa IZ = 0.0 mm PMID[450170]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis IZ = 10.0 mm PMID[450170]
NPT3473 Organism Mycobacterium vaccae Mycobacterium vaccae IZ = 0.0 mm PMID[450170]
NPT3474 Organism Sporidiobolus salmonicolor Sporidiobolus salmonicolor IZ = 0.0 mm PMID[450170]
NPT20 Organism Candida albicans Candida albicans IZ = 0.0 mm PMID[450170]
NPT2242 Organism Penicillium chrysogenum Penicillium chrysogenum IZ = 0.0 mm PMID[450170]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus IZ = 0.0 mm PMID[450170]
NPT21 Organism Aspergillus niger Aspergillus niger IZ = 0.0 mm PMID[450170]
NPT184 Organism Aspergillus terreus Aspergillus terreus IZ = 0.0 mm PMID[450170]

☑ 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 NPC470663 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
0.9194 High Similarity NPC51166
0.8406 Intermediate Similarity NPC470662
0.6923 Remote Similarity NPC470664
0.6528 Remote Similarity NPC47333
0.6438 Remote Similarity NPC55068
0.6429 Remote Similarity NPC168308
0.6429 Remote Similarity NPC302569
0.6364 Remote Similarity NPC103712
0.6364 Remote Similarity NPC291196
0.6301 Remote Similarity NPC470665
0.629 Remote Similarity NPC46248
0.629 Remote Similarity NPC249801
0.625 Remote Similarity NPC288086
0.6184 Remote Similarity NPC113224
0.6076 Remote Similarity NPC324638
0.6049 Remote Similarity NPC470993
0.6049 Remote Similarity NPC470992
0.5976 Remote Similarity NPC3094
0.593 Remote Similarity NPC82799
0.5862 Remote Similarity NPC474312
0.5823 Remote Similarity NPC474812
0.5795 Remote Similarity NPC228638
0.5783 Remote Similarity NPC212008
0.5783 Remote Similarity NPC51055
0.5783 Remote Similarity NPC62293
0.5783 Remote Similarity NPC140327
0.5783 Remote Similarity NPC264417
0.5783 Remote Similarity NPC217095
0.5775 Remote Similarity NPC470666
0.5732 Remote Similarity NPC314678
0.573 Remote Similarity NPC470943
0.5676 Remote Similarity NPC321030
0.5641 Remote Similarity NPC477525
0.5634 Remote Similarity NPC474496
0.5632 Remote Similarity NPC79367
0.56 Remote Similarity NPC325550
0.56 Remote Similarity NPC329003
0.56 Remote Similarity NPC326524

  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 NPC470663 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
0.6438 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6076 Remote Similarity NPD3212 Clinical (unspecified phase)
0.573 Remote Similarity NPD9640 Clinical (unspecified phase)

  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