Structure

Physi-Chem Properties

Molecular Weight:  321.18
Volume:  345.232
LogP:  2.106
LogD:  2.164
LogS:  -3.583
# Rotatable Bonds:  10
TPSA:  50.19
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.508
Synthetic Accessibility Score:  3.747
Fsp3:  0.556
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:  -4.784
MDCK Permeability:  3.181697320542298e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.154
Plasma Protein Binding (PPB):  85.82030487060547%
Volume Distribution (VD):  0.551
Pgp-substrate:  7.009378910064697%

ADMET: Metabolism

CYP1A2-inhibitor:  0.898
CYP1A2-substrate:  0.948
CYP2C19-inhibitor:  0.824
CYP2C19-substrate:  0.421
CYP2C9-inhibitor:  0.484
CYP2C9-substrate:  0.946
CYP2D6-inhibitor:  0.257
CYP2D6-substrate:  0.901
CYP3A4-inhibitor:  0.749
CYP3A4-substrate:  0.514

ADMET: Excretion

Clearance (CL):  9.814
Half-life (T1/2):  0.875

ADMET: Toxicity

hERG Blockers:  0.035
Human Hepatotoxicity (H-HT):  0.836
Drug-inuced Liver Injury (DILI):  0.478
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.055
Maximum Recommended Daily Dose:  0.826
Skin Sensitization:  0.314
Carcinogencity:  0.762
Eye Corrosion:  0.009
Eye Irritation:  0.12
Respiratory Toxicity:  0.932

Download Data

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

  Natural Product: NPC475568

Natural Product ID:  NPC475568
Common Name*:   (4S,11S)-11-Hydroxy-4-Methyl-13-(2-Methylthiazol-4-Yl)Trideca-8,12-Dien-3-One
IUPAC Name:   (4S,8Z,11S,12E)-11-hydroxy-4-methyl-13-(2-methyl-1,3-thiazol-4-yl)trideca-8,12-dien-3-one
Synonyms:  
Standard InCHIKey:  HYNDSRJYSBDNCW-JRHHNZPPSA-N
Standard InCHI:  InChI=1S/C18H27NO2S/c1-4-18(21)14(2)9-7-5-6-8-10-17(20)12-11-16-13-22-15(3)19-16/h6,8,11-14,17,20H,4-5,7,9-10H2,1-3H3/b8-6-,12-11+/t14-,17-/m0/s1
SMILES:  CCC(=O)C(C)CCCC=CCC(C=CC1=CSC(=N1)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL508397
PubChem CID:   44559969
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000436] Azoles
        • [CHEMONTID:0000095] Thiazoles
          • [CHEMONTID:0002634] 2,4-disubstituted thiazoles

*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
NPO32627 sorangium cellulosum, strains so ce90/b2 Species Polyangiaceae Bacteria n.a. n.a. n.a. PMID[11473410]

☑ 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
NPT1460 Cell Line L929 Mus musculus IC50 > 4.0 ug.mL-1 PMID[477149]

☑ 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 NPC475568 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
0.9748 High Similarity NPC475604
0.9206 High Similarity NPC474070
0.8456 Intermediate Similarity NPC474069
0.8214 Intermediate Similarity NPC474102
0.8214 Intermediate Similarity NPC157194
0.8214 Intermediate Similarity NPC475683
0.8214 Intermediate Similarity NPC474079
0.8214 Intermediate Similarity NPC21449
0.8214 Intermediate Similarity NPC474080
0.8169 Intermediate Similarity NPC224609
0.8169 Intermediate Similarity NPC268063
0.8156 Intermediate Similarity NPC474067
0.8143 Intermediate Similarity NPC474103
0.8143 Intermediate Similarity NPC474068
0.8143 Intermediate Similarity NPC474064
0.8143 Intermediate Similarity NPC82436
0.8099 Intermediate Similarity NPC32583
0.8099 Intermediate Similarity NPC252616
0.8099 Intermediate Similarity NPC163147
0.8099 Intermediate Similarity NPC45576
0.8099 Intermediate Similarity NPC474090
0.8099 Intermediate Similarity NPC61667
0.8099 Intermediate Similarity NPC154873
0.8099 Intermediate Similarity NPC109498
0.8028 Intermediate Similarity NPC475737
0.8028 Intermediate Similarity NPC185665
0.8028 Intermediate Similarity NPC474094
0.8 Intermediate Similarity NPC127775
0.7862 Intermediate Similarity NPC202591
0.7847 Intermediate Similarity NPC206724
0.7847 Intermediate Similarity NPC474515
0.7755 Intermediate Similarity NPC315252
0.7755 Intermediate Similarity NPC52587
0.774 Intermediate Similarity NPC212214
0.7687 Intermediate Similarity NPC21126
0.7635 Intermediate Similarity NPC474538
0.7584 Intermediate Similarity NPC231110
0.7533 Intermediate Similarity NPC312887
0.7361 Intermediate Similarity NPC190329
0.7103 Intermediate Similarity NPC469801
0.7075 Intermediate Similarity NPC319751
0.6933 Remote Similarity NPC119481
0.6867 Remote Similarity NPC473398
0.6503 Remote Similarity NPC476103
0.6369 Remote Similarity NPC14101
0.6343 Remote Similarity NPC165538
0.6341 Remote Similarity NPC97078
0.6341 Remote Similarity NPC470146
0.6341 Remote Similarity NPC24990
0.6341 Remote Similarity NPC101980
0.6322 Remote Similarity NPC122427
0.631 Remote Similarity NPC475534
0.631 Remote Similarity NPC476080
0.631 Remote Similarity NPC161242
0.6229 Remote Similarity NPC329961
0.6209 Remote Similarity NPC478251
0.6209 Remote Similarity NPC478252
0.6176 Remote Similarity NPC475330
0.614 Remote Similarity NPC263485
0.614 Remote Similarity NPC229160
0.614 Remote Similarity NPC174652
0.614 Remote Similarity NPC25316
0.6129 Remote Similarity NPC475390
0.6028 Remote Similarity NPC214375
0.6024 Remote Similarity NPC473886
0.6014 Remote Similarity NPC278902
0.6011 Remote Similarity NPC14877
0.6011 Remote Similarity NPC475350
0.6011 Remote Similarity NPC145178
0.6 Remote Similarity NPC96016
0.5931 Remote Similarity NPC267605
0.5916 Remote Similarity NPC251036
0.5886 Remote Similarity NPC161143
0.5833 Remote Similarity NPC135558
0.5772 Remote Similarity NPC89592
0.5754 Remote Similarity NPC238242
0.5752 Remote Similarity NPC478254
0.5752 Remote Similarity NPC478253
0.5714 Remote Similarity NPC51692
0.5682 Remote Similarity NPC249662
0.5661 Remote Similarity NPC75498
0.5655 Remote Similarity NPC211555
0.5655 Remote Similarity NPC56058
0.5655 Remote Similarity NPC522
0.5652 Remote Similarity NPC239660
0.5652 Remote Similarity NPC106235
0.5621 Remote Similarity NPC74917
0.5614 Remote Similarity NPC475920
0.5612 Remote Similarity NPC190955

  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 NPC475568 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
0.8028 Intermediate Similarity NPD6907 Phase 2
0.7687 Intermediate Similarity NPD6910 Phase 3
0.75 Intermediate Similarity NPD6915 Approved
0.745 Intermediate Similarity NPD6911 Discontinued
0.729 Intermediate Similarity NPD6916 Clinical (unspecified phase)
0.6645 Remote Similarity NPD5189 Clinical (unspecified phase)
0.6566 Remote Similarity NPD2957 Phase 2
0.6561 Remote Similarity NPD5634 Approved
0.6552 Remote Similarity NPD1083 Clinical (unspecified phase)
0.6023 Remote Similarity NPD6632 Clinical (unspecified phase)
0.5975 Remote Similarity NPD1004 Phase 2
0.5975 Remote Similarity NPD1005 Phase 2
0.5886 Remote Similarity NPD1745 Approved
0.5882 Remote Similarity NPD647 Approved
0.5825 Remote Similarity NPD7496 Phase 2
0.5795 Remote Similarity NPD7977 Clinical (unspecified phase)
0.5747 Remote Similarity NPD5755 Clinical (unspecified phase)
0.5652 Remote Similarity NPD8339 Clinical (unspecified phase)
0.5604 Remote Similarity NPD6348 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