Structure

Physi-Chem Properties

Molecular Weight:  335.19
Volume:  362.528
LogP:  2.582
LogD:  2.823
LogS:  -3.941
# 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:  0.616
Synthetic Accessibility Score:  3.822
Fsp3:  0.579
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:  -4.742
MDCK Permeability:  2.5939460101653822e-05
Pgp-inhibitor:  0.064
Pgp-substrate:  0.025
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.997
30% Bioavailability (F30%):  0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.216
Plasma Protein Binding (PPB):  87.22419738769531%
Volume Distribution (VD):  0.815
Pgp-substrate:  4.726065635681152%

ADMET: Metabolism

CYP1A2-inhibitor:  0.883
CYP1A2-substrate:  0.943
CYP2C19-inhibitor:  0.843
CYP2C19-substrate:  0.408
CYP2C9-inhibitor:  0.666
CYP2C9-substrate:  0.944
CYP2D6-inhibitor:  0.37
CYP2D6-substrate:  0.893
CYP3A4-inhibitor:  0.737
CYP3A4-substrate:  0.542

ADMET: Excretion

Clearance (CL):  9.947
Half-life (T1/2):  0.788

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.854
Drug-inuced Liver Injury (DILI):  0.558
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.032
Maximum Recommended Daily Dose:  0.821
Skin Sensitization:  0.1
Carcinogencity:  0.405
Eye Corrosion:  0.009
Eye Irritation:  0.14
Respiratory Toxicity:  0.817

Download Data

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

  Natural Product: NPC475604

Natural Product ID:  NPC475604
Common Name*:   (4S,8Z,11S,12E)-11-Hydroxy-4,8-Dimethyl-13-(2-Methylthiazol-4-Yl)Trideca-8,12-Dien-3-One
IUPAC Name:   (4S,8Z,11S,12E)-11-hydroxy-4,8-dimethyl-13-(2-methyl-1,3-thiazol-4-yl)trideca-8,12-dien-3-one
Synonyms:  
Standard InCHIKey:  BSUTWIMCWXXFTI-FWOSSDJBSA-N
Standard InCHI:  InChI=1S/C19H29NO2S/c1-5-19(22)15(3)8-6-7-14(2)9-11-18(21)12-10-17-13-23-16(4)20-17/h9-10,12-13,15,18,21H,5-8,11H2,1-4H3/b12-10+,14-9-/t15-,18-/m0/s1
SMILES:  CCC(=O)C(C)CCCC(=CCC(C=CC1=CSC(=N1)C)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL509097
PubChem CID:   44559970
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[537647]

☑ 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 NPC475604 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 NPC475568
0.9291 High Similarity NPC474070
0.854 High Similarity NPC474069
0.8429 Intermediate Similarity NPC21449
0.8429 Intermediate Similarity NPC475683
0.8429 Intermediate Similarity NPC474079
0.8429 Intermediate Similarity NPC157194
0.8429 Intermediate Similarity NPC474102
0.8429 Intermediate Similarity NPC474080
0.838 Intermediate Similarity NPC224609
0.838 Intermediate Similarity NPC268063
0.8357 Intermediate Similarity NPC474068
0.8357 Intermediate Similarity NPC474064
0.8357 Intermediate Similarity NPC82436
0.8357 Intermediate Similarity NPC474103
0.831 Intermediate Similarity NPC154873
0.831 Intermediate Similarity NPC109498
0.831 Intermediate Similarity NPC474090
0.831 Intermediate Similarity NPC252616
0.831 Intermediate Similarity NPC45576
0.831 Intermediate Similarity NPC32583
0.831 Intermediate Similarity NPC61667
0.831 Intermediate Similarity NPC163147
0.8239 Intermediate Similarity NPC475737
0.8239 Intermediate Similarity NPC474067
0.8239 Intermediate Similarity NPC185665
0.8239 Intermediate Similarity NPC474094
0.8207 Intermediate Similarity NPC127775
0.8056 Intermediate Similarity NPC474515
0.8056 Intermediate Similarity NPC206724
0.7959 Intermediate Similarity NPC52587
0.7959 Intermediate Similarity NPC315252
0.7945 Intermediate Similarity NPC212214
0.7945 Intermediate Similarity NPC202591
0.7891 Intermediate Similarity NPC21126
0.7838 Intermediate Similarity NPC474538
0.7785 Intermediate Similarity NPC231110
0.7733 Intermediate Similarity NPC312887
0.7569 Intermediate Similarity NPC190329
0.7075 Intermediate Similarity NPC469801
0.7047 Intermediate Similarity NPC319751
0.6908 Remote Similarity NPC119481
0.6842 Remote Similarity NPC473398
0.6485 Remote Similarity NPC476103
0.642 Remote Similarity NPC165538
0.6325 Remote Similarity NPC97078
0.6325 Remote Similarity NPC470146
0.6325 Remote Similarity NPC24990
0.6325 Remote Similarity NPC101980
0.6307 Remote Similarity NPC122427
0.6299 Remote Similarity NPC478252
0.6299 Remote Similarity NPC478251
0.6294 Remote Similarity NPC161242
0.6294 Remote Similarity NPC476080
0.6294 Remote Similarity NPC475534
0.625 Remote Similarity NPC14101
0.6215 Remote Similarity NPC329961
0.6163 Remote Similarity NPC475330
0.6127 Remote Similarity NPC25316
0.6127 Remote Similarity NPC263485
0.6127 Remote Similarity NPC229160
0.6127 Remote Similarity NPC174652
0.6085 Remote Similarity NPC14877
0.6085 Remote Similarity NPC475350
0.6085 Remote Similarity NPC145178
0.6013 Remote Similarity NPC475390
0.6 Remote Similarity NPC278902
0.599 Remote Similarity NPC251036
0.5989 Remote Similarity NPC96016
0.5966 Remote Similarity NPC161143
0.5917 Remote Similarity NPC473886
0.5903 Remote Similarity NPC214375
0.5844 Remote Similarity NPC478254
0.5844 Remote Similarity NPC478253
0.5833 Remote Similarity NPC211555
0.5815 Remote Similarity NPC239660
0.5815 Remote Similarity NPC106235
0.5811 Remote Similarity NPC267605
0.5774 Remote Similarity NPC186452
0.5746 Remote Similarity NPC238242
0.574 Remote Similarity NPC56058
0.574 Remote Similarity NPC522
0.5737 Remote Similarity NPC75498
0.5714 Remote Similarity NPC135558
0.5674 Remote Similarity NPC249662
0.5658 Remote Similarity NPC89592
0.5647 Remote Similarity NPC210424
0.564 Remote Similarity NPC12660
0.5632 Remote Similarity NPC164006
0.5607 Remote Similarity NPC475920
0.5607 Remote Similarity NPC54983
0.5604 Remote Similarity NPC469858
0.56 Remote Similarity NPC51692

  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 NPC475604 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
0.8239 Intermediate Similarity NPD6907 Phase 2
0.7891 Intermediate Similarity NPD6910 Phase 3
0.7703 Intermediate Similarity NPD6915 Approved
0.7651 Intermediate Similarity NPD6911 Discontinued
0.7484 Intermediate Similarity NPD6916 Clinical (unspecified phase)
0.6624 Remote Similarity NPD5189 Clinical (unspecified phase)
0.6548 Remote Similarity NPD2957 Phase 2
0.6541 Remote Similarity NPD5634 Approved
0.6531 Remote Similarity NPD1083 Clinical (unspecified phase)
0.6102 Remote Similarity NPD6632 Clinical (unspecified phase)
0.6062 Remote Similarity NPD1004 Phase 2
0.6062 Remote Similarity NPD1005 Phase 2
0.5979 Remote Similarity NPD7496 Phase 2
0.592 Remote Similarity NPD5755 Clinical (unspecified phase)
0.5876 Remote Similarity NPD7977 Clinical (unspecified phase)
0.5876 Remote Similarity NPD1745 Approved
0.5872 Remote Similarity NPD647 Approved
0.5815 Remote Similarity NPD8339 Clinical (unspecified phase)
0.5769 Remote Similarity NPD6348 Clinical (unspecified phase)
0.5738 Remote Similarity NPD4949 Discontinued
0.5714 Remote Similarity NPD6349 Phase 1

  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