Structure

Physi-Chem Properties

Molecular Weight:  267.18
Volume:  288.898
LogP:  5.048
LogD:  3.819
LogS:  -3.582
# Rotatable Bonds:  9
TPSA:  73.32
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.466
Synthetic Accessibility Score:  2.599
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.785
MDCK Permeability:  2.3710223103989847e-05
Pgp-inhibitor:  0.007
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.995
30% Bioavailability (F30%):  0.75

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.279
Plasma Protein Binding (PPB):  98.35382080078125%
Volume Distribution (VD):  0.888
Pgp-substrate:  1.6750881671905518%

ADMET: Metabolism

CYP1A2-inhibitor:  0.859
CYP1A2-substrate:  0.878
CYP2C19-inhibitor:  0.707
CYP2C19-substrate:  0.066
CYP2C9-inhibitor:  0.604
CYP2C9-substrate:  0.916
CYP2D6-inhibitor:  0.864
CYP2D6-substrate:  0.59
CYP3A4-inhibitor:  0.436
CYP3A4-substrate:  0.115

ADMET: Excretion

Clearance (CL):  3.042
Half-life (T1/2):  0.607

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.184
Drug-inuced Liver Injury (DILI):  0.906
AMES Toxicity:  0.027
Rat Oral Acute Toxicity:  0.621
Maximum Recommended Daily Dose:  0.027
Skin Sensitization:  0.612
Carcinogencity:  0.246
Eye Corrosion:  0.004
Eye Irritation:  0.647
Respiratory Toxicity:  0.927

Download Data

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

  Natural Product: NPC469835

Natural Product ID:  NPC469835
Common Name*:   KHTHQNHXMCUIBE-IBPBOOLHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KHTHQNHXMCUIBE-IBPBOOLHSA-N
Standard InCHI:  InChI=1S/C15H25NO3/c1-3-4-5-6-7-8-9-10-12(17)13-14(18)11(2)16-15(13)19/h11,17H,3-10H2,1-2H3,(H,16,19)/b13-12-/t11-/m0/s1
SMILES:  CCCCCCCCC/C(=C1/C(=N[C@H](C1=O)C)O)/O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1213027
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines
        • [CHEMONTID:0001158] Pyrrolidones
          • [CHEMONTID:0003032] Pyrrolidine-3-ones

*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
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[10556916]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[19406895]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[19917748]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[20932054]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[25043228]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[25960261]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[32603106]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. Antarctic n.a. PMID[8882433]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]

☑ 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 100000.0 nM PMID[511312]
NPT2 Others Unspecified IC50 = 20000.0 nM PMID[511312]

☑ 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 NPC469835 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
0.9706 High Similarity NPC469836
0.8947 High Similarity NPC469833
0.8947 High Similarity NPC469838
0.8219 Intermediate Similarity NPC4706
0.7037 Intermediate Similarity NPC263266
0.6771 Remote Similarity NPC313234
0.6633 Remote Similarity NPC474563
0.6476 Remote Similarity NPC476813
0.6476 Remote Similarity NPC476814
0.6429 Remote Similarity NPC175531
0.6373 Remote Similarity NPC140251
0.6373 Remote Similarity NPC307903
0.6234 Remote Similarity NPC29468
0.6216 Remote Similarity NPC40148
0.6207 Remote Similarity NPC477485
0.6163 Remote Similarity NPC477484
0.6163 Remote Similarity NPC46268
0.6163 Remote Similarity NPC477486
0.6129 Remote Similarity NPC34754
0.6098 Remote Similarity NPC45060
0.6098 Remote Similarity NPC291196
0.6098 Remote Similarity NPC280065
0.6098 Remote Similarity NPC103712
0.604 Remote Similarity NPC469598
0.6 Remote Similarity NPC24389
0.5978 Remote Similarity NPC319913
0.596 Remote Similarity NPC4834
0.5949 Remote Similarity NPC316674
0.5943 Remote Similarity NPC476290
0.5926 Remote Similarity NPC187315
0.5922 Remote Similarity NPC472616
0.5921 Remote Similarity NPC192843
0.5914 Remote Similarity NPC322672
0.5897 Remote Similarity NPC130807
0.5897 Remote Similarity NPC6795
0.5851 Remote Similarity NPC472614
0.5851 Remote Similarity NPC473525
0.5843 Remote Similarity NPC471597
0.5841 Remote Similarity NPC469515
0.5833 Remote Similarity NPC476269
0.5824 Remote Similarity NPC474312
0.5824 Remote Similarity NPC473810
0.5814 Remote Similarity NPC288086
0.5783 Remote Similarity NPC249713
0.5761 Remote Similarity NPC471595
0.573 Remote Similarity NPC469492
0.5714 Remote Similarity NPC281230
0.5714 Remote Similarity NPC471022
0.5714 Remote Similarity NPC472615
0.5714 Remote Similarity NPC245650
0.57 Remote Similarity NPC175614
0.5698 Remote Similarity NPC144419
0.569 Remote Similarity NPC469494
0.5667 Remote Similarity NPC469517
0.566 Remote Similarity NPC475800
0.5657 Remote Similarity NPC116930
0.5652 Remote Similarity NPC39966
0.5648 Remote Similarity NPC113012
0.5648 Remote Similarity NPC122926
0.5632 Remote Similarity NPC7382
0.5631 Remote Similarity NPC474873
0.5625 Remote Similarity NPC476190
0.5625 Remote Similarity NPC273614
0.5612 Remote Similarity NPC472264
0.561 Remote Similarity NPC477525
0.56 Remote Similarity NPC469424

  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 NPC469835 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