Structure

Physi-Chem Properties

Molecular Weight:  665.12
Volume:  550.23
LogP:  -3.91
LogD:  -1.523
LogS:  -0.858
# Rotatable Bonds:  11
TPSA:  312.03
# H-Bond Aceptor:  21
# H-Bond Donor:  8
# Rings:  5
# Heavy Atoms:  23

MedChem Properties

QED Drug-Likeness Score:  0.122
Synthetic Accessibility Score:  6.251
Fsp3:  0.524
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.329
MDCK Permeability:  1.123152924265014e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.892
Human Intestinal Absorption (HIA):  0.991
20% Bioavailability (F20%):  0.981
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.78
Plasma Protein Binding (PPB):  14.04874038696289%
Volume Distribution (VD):  0.318
Pgp-substrate:  66.04692077636719%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.075
CYP2C19-inhibitor:  0.044
CYP2C19-substrate:  0.028
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.176
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.055
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.003

ADMET: Excretion

Clearance (CL):  1.464
Half-life (T1/2):  0.772

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.154
Drug-inuced Liver Injury (DILI):  0.843
AMES Toxicity:  0.072
Rat Oral Acute Toxicity:  0.278
Maximum Recommended Daily Dose:  0.921
Skin Sensitization:  0.099
Carcinogencity:  0.389
Eye Corrosion:  0.003
Eye Irritation:  0.005
Respiratory Toxicity:  0.81

Download Data

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

  Natural Product: NPC470662

Natural Product ID:  NPC470662
Common Name*:   Elaiomycin D
IUPAC Name:   n.a.
Synonyms:   Elaiomycin D
Standard InCHIKey:  BRLWDWOZGPKZAD-XLTRDJIWSA-N
Standard InCHI:  InChI=1S/C13H24N2O4/c1-11(16)8-6-4-5-7-9-15(18)14-13(10-19-3)12(2)17/h7,9,12-13,17H,4-6,8,10H2,1-3H3/b9-7+,15-14-/t12-,13-/m0/s1
SMILES:  COC[C@@H]([C@@H](O)C)/N=N(O)/C=C/CCCCC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2152469
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 > 50.0 ug.mL-1 PMID[551074]
NPT111 Cell Line K562 Homo sapiens GI50 > 50.0 ug.mL-1 PMID[551074]
NPT165 Cell Line HeLa Homo sapiens CC50 > 50.0 ug.mL-1 PMID[551074]
NPT79 Organism Bacillus subtilis Bacillus subtilis IZ = 0.0 mm PMID[551074]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 0.0 mm PMID[551074]
NPT19 Organism Escherichia coli Escherichia coli IZ = 0.0 mm PMID[551074]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa IZ = 0.0 mm PMID[551074]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis IZ = 0.0 mm PMID[551074]
NPT3473 Organism Mycobacterium vaccae Mycobacterium vaccae IZ = 0.0 mm PMID[551074]
NPT3474 Organism Sporidiobolus salmonicolor Sporidiobolus salmonicolor IZ = 0.0 mm PMID[551074]
NPT20 Organism Candida albicans Candida albicans IZ = 0.0 mm PMID[551074]
NPT2242 Organism Penicillium chrysogenum Penicillium chrysogenum IZ = 0.0 mm PMID[551074]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus IZ = 0.0 mm PMID[551074]
NPT21 Organism Aspergillus niger Aspergillus niger IZ = 0.0 mm PMID[551074]
NPT184 Organism Aspergillus terreus Aspergillus terreus IZ = 0.0 mm PMID[551074]

☑ 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 NPC470662 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
0.8769 High Similarity NPC51166
0.8406 Intermediate Similarity NPC470663
0.7681 Intermediate Similarity NPC470665
0.6618 Remote Similarity NPC470664
0.6067 Remote Similarity NPC470943
0.5857 Remote Similarity NPC473487
0.5854 Remote Similarity NPC97614
0.5844 Remote Similarity NPC47333
0.5843 Remote Similarity NPC474312
0.5823 Remote Similarity NPC296436
0.5823 Remote Similarity NPC176215
0.5769 Remote Similarity NPC55068
0.5733 Remote Similarity NPC302569
0.5733 Remote Similarity NPC168308
0.5694 Remote Similarity NPC473705
0.5647 Remote Similarity NPC470993
0.5647 Remote Similarity NPC470992
0.561 Remote Similarity NPC474812

  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 NPC470662 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
0.5769 Remote Similarity NPD3210 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