Structure

Physi-Chem Properties

Molecular Weight:  213.14
Volume:  222.35
LogP:  1.824
LogD:  1.543
LogS:  -2.131
# Rotatable Bonds:  7
TPSA:  55.4
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.536
Synthetic Accessibility Score:  2.546
Fsp3:  0.818
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:  -4.517
MDCK Permeability:  4.641266059479676e-05
Pgp-inhibitor:  0.32
Pgp-substrate:  0.019
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.306
30% Bioavailability (F30%):  0.974

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.99
Plasma Protein Binding (PPB):  36.11146926879883%
Volume Distribution (VD):  0.731
Pgp-substrate:  68.14012145996094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.257
CYP1A2-substrate:  0.324
CYP2C19-inhibitor:  0.383
CYP2C19-substrate:  0.427
CYP2C9-inhibitor:  0.156
CYP2C9-substrate:  0.299
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.193
CYP3A4-inhibitor:  0.127
CYP3A4-substrate:  0.231

ADMET: Excretion

Clearance (CL):  6.791
Half-life (T1/2):  0.716

ADMET: Toxicity

hERG Blockers:  0.033
Human Hepatotoxicity (H-HT):  0.055
Drug-inuced Liver Injury (DILI):  0.071
AMES Toxicity:  0.029
Rat Oral Acute Toxicity:  0.015
Maximum Recommended Daily Dose:  0.059
Skin Sensitization:  0.454
Carcinogencity:  0.254
Eye Corrosion:  0.011
Eye Irritation:  0.139
Respiratory Toxicity:  0.045

Download Data

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

  Natural Product: NPC477644

Natural Product ID:  NPC477644
Common Name*:   N-Heptanoyl-DL-homoserine lactone
IUPAC Name:   N-(2-oxooxolan-3-yl)heptanamide
Synonyms:  
Standard InCHIKey:  FTMZLSDESAOPSZ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H19NO3/c1-2-3-4-5-6-10(13)12-9-7-8-15-11(9)14/h9H,2-8H2,1H3,(H,12,13)
SMILES:  CCCCCCC(=O)NC1CCOC1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5057188
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:0001189] N-acyl-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
NPO33619 Pantoea ananatis Species Erwiniaceae Bacteria n.a. n.a. n.a. PMID[18465897]

☑ 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
NPT79 Organism Bacillus subtilis Bacillus subtilis Activity = 500 ug/ml PMID[18465897]

☑ 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 NPC477644 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
0.875 High Similarity NPC477642
0.8689 High Similarity NPC145658
0.8485 Intermediate Similarity NPC320865
0.8485 Intermediate Similarity NPC477641
0.8485 Intermediate Similarity NPC477643
0.8033 Intermediate Similarity NPC473599
0.75 Intermediate Similarity NPC474298
0.75 Intermediate Similarity NPC473985
0.75 Intermediate Similarity NPC474299
0.75 Intermediate Similarity NPC475808
0.75 Intermediate Similarity NPC28348
0.7313 Intermediate Similarity NPC470108
0.7288 Intermediate Similarity NPC329181
0.7288 Intermediate Similarity NPC319110
0.7206 Intermediate Similarity NPC470109
0.7143 Intermediate Similarity NPC478256
0.7101 Intermediate Similarity NPC470110
0.7083 Intermediate Similarity NPC43219
0.6986 Remote Similarity NPC86064
0.6923 Remote Similarity NPC254541
0.6835 Remote Similarity NPC155670
0.6835 Remote Similarity NPC95478
0.6835 Remote Similarity NPC145748
0.6769 Remote Similarity NPC189301
0.6769 Remote Similarity NPC176164
0.6765 Remote Similarity NPC57420
0.675 Remote Similarity NPC227051
0.6667 Remote Similarity NPC227850
0.6667 Remote Similarity NPC476285
0.6667 Remote Similarity NPC476291
0.6667 Remote Similarity NPC320598
0.6618 Remote Similarity NPC327252
0.6613 Remote Similarity NPC322946
0.6585 Remote Similarity NPC477728
0.6528 Remote Similarity NPC474812
0.65 Remote Similarity NPC289484
0.65 Remote Similarity NPC319709
0.6486 Remote Similarity NPC141325
0.6486 Remote Similarity NPC474403
0.6418 Remote Similarity NPC321468
0.6418 Remote Similarity NPC317143
0.6418 Remote Similarity NPC316826
0.6418 Remote Similarity NPC327748
0.6406 Remote Similarity NPC316889
0.6406 Remote Similarity NPC321118
0.64 Remote Similarity NPC138435
0.64 Remote Similarity NPC476248
0.6364 Remote Similarity NPC317147
0.6364 Remote Similarity NPC318260
0.6353 Remote Similarity NPC477729
0.6349 Remote Similarity NPC19576
0.6349 Remote Similarity NPC29950
0.6324 Remote Similarity NPC327170
0.6324 Remote Similarity NPC329564
0.6316 Remote Similarity NPC472595
0.6308 Remote Similarity NPC327831
0.6308 Remote Similarity NPC322573
0.6308 Remote Similarity NPC471917
0.6301 Remote Similarity NPC314273
0.6301 Remote Similarity NPC193280
0.6296 Remote Similarity NPC474312
0.6296 Remote Similarity NPC477730
0.625 Remote Similarity NPC263065
0.625 Remote Similarity NPC189178
0.6234 Remote Similarity NPC476324
0.6234 Remote Similarity NPC476130
0.6212 Remote Similarity NPC38463
0.619 Remote Similarity NPC327239
0.6176 Remote Similarity NPC319991
0.6176 Remote Similarity NPC321536
0.6154 Remote Similarity NPC472594
0.6154 Remote Similarity NPC270041
0.6129 Remote Similarity NPC153370
0.6087 Remote Similarity NPC143722
0.6076 Remote Similarity NPC316242
0.6066 Remote Similarity NPC297220
0.6056 Remote Similarity NPC315744
0.6056 Remote Similarity NPC316674
0.6049 Remote Similarity NPC314466
0.6047 Remote Similarity NPC292345
0.6032 Remote Similarity NPC328378
0.6023 Remote Similarity NPC208537
0.6023 Remote Similarity NPC270005
0.6 Remote Similarity NPC474833
0.6 Remote Similarity NPC478017
0.6 Remote Similarity NPC315535
0.6 Remote Similarity NPC473984
0.6 Remote Similarity NPC315131
0.597 Remote Similarity NPC325985
0.5932 Remote Similarity NPC241279
0.5915 Remote Similarity NPC145627
0.5893 Remote Similarity NPC80641
0.5882 Remote Similarity NPC278209
0.5862 Remote Similarity NPC327250
0.5857 Remote Similarity NPC321419
0.5844 Remote Similarity NPC315897
0.5844 Remote Similarity NPC55274
0.5806 Remote Similarity NPC306238
0.5806 Remote Similarity NPC52700
0.5806 Remote Similarity NPC105329
0.5806 Remote Similarity NPC220234
0.5806 Remote Similarity NPC145045
0.5806 Remote Similarity NPC248970
0.5806 Remote Similarity NPC63182
0.5795 Remote Similarity NPC159369
0.5795 Remote Similarity NPC475801
0.5795 Remote Similarity NPC39290
0.5795 Remote Similarity NPC474593
0.5789 Remote Similarity NPC45060
0.5789 Remote Similarity NPC280065
0.5758 Remote Similarity NPC329495
0.5758 Remote Similarity NPC197087
0.5758 Remote Similarity NPC190184
0.5753 Remote Similarity NPC160661
0.5753 Remote Similarity NPC174304
0.5753 Remote Similarity NPC325597
0.5753 Remote Similarity NPC472609
0.5735 Remote Similarity NPC313263
0.573 Remote Similarity NPC474576
0.5714 Remote Similarity NPC136159
0.5714 Remote Similarity NPC47135
0.5714 Remote Similarity NPC325734
0.5694 Remote Similarity NPC17455
0.5682 Remote Similarity NPC193386
0.5679 Remote Similarity NPC37681
0.5679 Remote Similarity NPC233108
0.5676 Remote Similarity NPC474402
0.5667 Remote Similarity NPC173763
0.5667 Remote Similarity NPC471098
0.5667 Remote Similarity NPC62263
0.5663 Remote Similarity NPC475542
0.5658 Remote Similarity NPC472579
0.5645 Remote Similarity NPC327698
0.5645 Remote Similarity NPC273545
0.5645 Remote Similarity NPC118459
0.5634 Remote Similarity NPC471129
0.5625 Remote Similarity NPC5864
0.5625 Remote Similarity NPC124554
0.5625 Remote Similarity NPC301148
0.5616 Remote Similarity NPC289691

  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 NPC477644 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
0.875 High Similarity NPD9419 Clinical (unspecified phase)
0.8485 Intermediate Similarity NPD2256 Clinical (unspecified phase)
0.7 Intermediate Similarity NPD3724 Clinical (unspecified phase)
0.6716 Remote Similarity NPD574 Approved
0.6714 Remote Similarity NPD2263 Discontinued
0.6618 Remote Similarity NPD575 Clinical (unspecified phase)
0.6613 Remote Similarity NPD9441 Phase 2
0.6582 Remote Similarity NPD1448 Clinical (unspecified phase)
0.65 Remote Similarity NPD3211 Approved
0.6494 Remote Similarity NPD3160 Suspended
0.6349 Remote Similarity NPD8846 Approved
0.6349 Remote Similarity NPD8847 Approved
0.6349 Remote Similarity NPD61 Approved
0.6333 Remote Similarity NPD1152 Phase 2
0.6269 Remote Similarity NPD9433 Approved
0.6267 Remote Similarity NPD6944 Clinical (unspecified phase)
0.625 Remote Similarity NPD9204 Approved
0.625 Remote Similarity NPD1429 Clinical (unspecified phase)
0.625 Remote Similarity NPD9205 Approved
0.6234 Remote Similarity NPD1453 Phase 1
0.6129 Remote Similarity NPD8614 Approved
0.6067 Remote Similarity NPD8394 Approved
0.6056 Remote Similarity NPD364 Discontinued
0.6047 Remote Similarity NPD618 Clinical (unspecified phase)
0.6 Remote Similarity NPD7918 Clinical (unspecified phase)
0.6 Remote Similarity NPD7917 Clinical (unspecified phase)
0.5949 Remote Similarity NPD2689 Clinical (unspecified phase)
0.5938 Remote Similarity NPD329 Discontinued
0.5904 Remote Similarity NPD883 Phase 2
0.5904 Remote Similarity NPD882 Phase 2
0.5902 Remote Similarity NPD9658 Clinical (unspecified phase)
0.5867 Remote Similarity NPD1815 Discontinued
0.5844 Remote Similarity NPD1825 Clinical (unspecified phase)
0.5811 Remote Similarity NPD5380 Approved
0.5811 Remote Similarity NPD886 Clinical (unspecified phase)
0.5806 Remote Similarity NPD8870 Approved
0.5789 Remote Similarity NPD2695 Approved
0.5789 Remote Similarity NPD2696 Approved
0.5789 Remote Similarity NPD2697 Approved
0.5789 Remote Similarity NPD2694 Approved
0.5781 Remote Similarity NPD9016 Clinical (unspecified phase)
0.5758 Remote Similarity NPD8785 Approved
0.5753 Remote Similarity NPD348 Approved
0.5733 Remote Similarity NPD9451 Clinical (unspecified phase)
0.5714 Remote Similarity NPD2262 Clinical (unspecified phase)
0.5714 Remote Similarity NPD7345 Approved
0.5714 Remote Similarity NPD1458 Approved
0.5714 Remote Similarity NPD1459 Approved
0.5714 Remote Similarity NPD9446 Approved
0.5698 Remote Similarity NPD619 Phase 3
0.5672 Remote Similarity NPD630 Approved
0.5672 Remote Similarity NPD631 Approved
0.5641 Remote Similarity NPD1147 Phase 2
0.5625 Remote Similarity NPD9213 Approved
0.5625 Remote Similarity NPD9214 Phase 3
0.5618 Remote Similarity NPD3716 Discontinued
0.5604 Remote Similarity NPD5781 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