Structure

Physi-Chem Properties

Molecular Weight:  419.18
Volume:  426.957
LogP:  3.522
LogD:  2.03
LogS:  -4.461
# Rotatable Bonds:  5
TPSA:  80.75
# H-Bond Aceptor:  6
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.386
Synthetic Accessibility Score:  5.104
Fsp3:  0.545
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.622
MDCK Permeability:  7.88355009717634e-06
Pgp-inhibitor:  0.014
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.087
20% Bioavailability (F20%):  0.307
30% Bioavailability (F30%):  0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.285
Plasma Protein Binding (PPB):  93.873779296875%
Volume Distribution (VD):  0.481
Pgp-substrate:  3.345327377319336%

ADMET: Metabolism

CYP1A2-inhibitor:  0.036
CYP1A2-substrate:  0.163
CYP2C19-inhibitor:  0.638
CYP2C19-substrate:  0.477
CYP2C9-inhibitor:  0.398
CYP2C9-substrate:  0.911
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.138
CYP3A4-inhibitor:  0.732
CYP3A4-substrate:  0.718

ADMET: Excretion

Clearance (CL):  6.468
Half-life (T1/2):  0.864

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.852
Drug-inuced Liver Injury (DILI):  0.949
AMES Toxicity:  0.92
Rat Oral Acute Toxicity:  0.213
Maximum Recommended Daily Dose:  0.963
Skin Sensitization:  0.953
Carcinogencity:  0.883
Eye Corrosion:  0.008
Eye Irritation:  0.02
Respiratory Toxicity:  0.973

Download Data

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

  Natural Product: NPC474985

Natural Product ID:  NPC474985
Common Name*:   (R)-3-Acetyl-4-(E)-4-(2R,5S,6Z,10Z)-5,10-Dimethyl-12-Oxooxacyclododeca-6,10-Dien-2-Yl)But-2-Enoyl)Thiazolidin-2-One
IUPAC Name:   (4R)-3-acetyl-4-[(E)-4-[(2R,5S,6Z,10Z)-5,10-dimethyl-12-oxo-1-oxacyclododeca-6,10-dien-2-yl]but-2-enoyl]-1,3-thiazolidin-2-one
Synonyms:  
Standard InCHIKey:  FISAKOWYJDPHMO-LVVBINIXSA-N
Standard InCHI:  InChI=1S/C22H29NO5S/c1-15-7-4-5-8-16(2)13-21(26)28-18(12-11-15)9-6-10-20(25)19-14-29-22(27)23(19)17(3)24/h4,6-7,10,13,15,18-19H,5,8-9,11-12,14H2,1-3H3/b7-4-,10-6+,16-13-/t15-,18+,19+/m1/s1
SMILES:  CC1CCC(OC(=O)C=C(CCC=C1)C)CC=CC(=O)C2CSC(=O)N2C(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL491169
PubChem CID:   11611475
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000147] Macrolides and analogues

*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
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. PMID[15217296]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. PMID[16499319]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. sand-covered bottom at -10 to -15 m at Hurghada, on the Egyptian Red Sea coast 2003-JUN PMID[18298079]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. PMID[18942825]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota 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
NPT314 Organism Bacillus cereus Bacillus cereus MIC = 17800.0 nM PMID[542265]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 17800.0 nM PMID[542265]
NPT20 Organism Candida albicans Candida albicans MIC = 2500.0 nM PMID[542265]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae MIC = 2500.0 nM PMID[542265]

☑ 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 NPC474985 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
0.7748 Intermediate Similarity NPC474984
0.7411 Intermediate Similarity NPC474995
0.6757 Remote Similarity NPC474244
0.6697 Remote Similarity NPC52820
0.6667 Remote Similarity NPC474873
0.6609 Remote Similarity NPC474099
0.6581 Remote Similarity NPC58281
0.6549 Remote Similarity NPC199831
0.6549 Remote Similarity NPC474827
0.6549 Remote Similarity NPC68001
0.6549 Remote Similarity NPC474828
0.6518 Remote Similarity NPC188785
0.65 Remote Similarity NPC471768
0.6496 Remote Similarity NPC127578
0.6435 Remote Similarity NPC101106
0.6435 Remote Similarity NPC135216
0.641 Remote Similarity NPC474891
0.6379 Remote Similarity NPC250187
0.6355 Remote Similarity NPC81195
0.6333 Remote Similarity NPC475988
0.6325 Remote Similarity NPC287572
0.6325 Remote Similarity NPC474969
0.6325 Remote Similarity NPC476034
0.6325 Remote Similarity NPC471636
0.6294 Remote Similarity NPC475342
0.6281 Remote Similarity NPC472536
0.6281 Remote Similarity NPC103391
0.625 Remote Similarity NPC268327
0.625 Remote Similarity NPC295444
0.625 Remote Similarity NPC476344
0.625 Remote Similarity NPC273215
0.625 Remote Similarity NPC279383
0.6226 Remote Similarity NPC469861
0.6226 Remote Similarity NPC130436
0.6226 Remote Similarity NPC469860
0.6216 Remote Similarity NPC150041
0.6214 Remote Similarity NPC277341
0.6214 Remote Similarity NPC226982
0.6207 Remote Similarity NPC205176
0.6146 Remote Similarity NPC470256
0.614 Remote Similarity NPC26597
0.6107 Remote Similarity NPC41162
0.6102 Remote Similarity NPC271562
0.6082 Remote Similarity NPC151481
0.6068 Remote Similarity NPC469604
0.6042 Remote Similarity NPC194871
0.6038 Remote Similarity NPC475975
0.6033 Remote Similarity NPC59249
0.6 Remote Similarity NPC117746
0.6 Remote Similarity NPC159568
0.6 Remote Similarity NPC259599
0.6 Remote Similarity NPC294434
0.6 Remote Similarity NPC15499
0.6 Remote Similarity NPC470300
0.6 Remote Similarity NPC476355
0.5968 Remote Similarity NPC477554
0.5952 Remote Similarity NPC470788
0.595 Remote Similarity NPC469603
0.5932 Remote Similarity NPC133420
0.592 Remote Similarity NPC477553
0.5918 Remote Similarity NPC476591
0.5918 Remote Similarity NPC88877
0.5882 Remote Similarity NPC123360
0.5882 Remote Similarity NPC93179
0.5873 Remote Similarity NPC476155
0.5873 Remote Similarity NPC477555
0.5873 Remote Similarity NPC17581
0.5872 Remote Similarity NPC324506
0.5865 Remote Similarity NPC178277
0.5865 Remote Similarity NPC270126
0.5859 Remote Similarity NPC469660
0.5856 Remote Similarity NPC17143
0.5856 Remote Similarity NPC47230
0.5849 Remote Similarity NPC173609
0.5846 Remote Similarity NPC97580
0.5842 Remote Similarity NPC140287
0.5842 Remote Similarity NPC474758
0.5833 Remote Similarity NPC470688
0.5833 Remote Similarity NPC319913
0.5825 Remote Similarity NPC471225
0.5825 Remote Similarity NPC57744
0.5821 Remote Similarity NPC120335
0.5816 Remote Similarity NPC96272
0.5806 Remote Similarity NPC193471
0.5806 Remote Similarity NPC130124
0.5804 Remote Similarity NPC299808
0.5804 Remote Similarity NPC118844
0.5804 Remote Similarity NPC72183
0.5804 Remote Similarity NPC110875
0.5802 Remote Similarity NPC309525
0.58 Remote Similarity NPC163003
0.5798 Remote Similarity NPC44514
0.5798 Remote Similarity NPC64168
0.5781 Remote Similarity NPC230849
0.578 Remote Similarity NPC322672
0.5773 Remote Similarity NPC248125
0.5772 Remote Similarity NPC469455
0.5772 Remote Similarity NPC21713
0.5772 Remote Similarity NPC168758
0.5772 Remote Similarity NPC475608
0.5772 Remote Similarity NPC47857
0.5772 Remote Similarity NPC181510
0.5769 Remote Similarity NPC108816
0.5769 Remote Similarity NPC93763
0.5769 Remote Similarity NPC128276
0.5763 Remote Similarity NPC473289
0.5758 Remote Similarity NPC470693
0.5755 Remote Similarity NPC471325
0.5755 Remote Similarity NPC281949
0.5755 Remote Similarity NPC301477
0.5755 Remote Similarity NPC42470
0.5755 Remote Similarity NPC25684
0.5748 Remote Similarity NPC174463
0.5738 Remote Similarity NPC329305
0.5727 Remote Similarity NPC473525
0.5714 Remote Similarity NPC264227
0.5714 Remote Similarity NPC472266
0.5714 Remote Similarity NPC203335
0.5714 Remote Similarity NPC6271
0.5714 Remote Similarity NPC279833
0.5714 Remote Similarity NPC472965
0.5714 Remote Similarity NPC80439
0.5714 Remote Similarity NPC63649
0.5714 Remote Similarity NPC173690
0.5701 Remote Similarity NPC473810
0.569 Remote Similarity NPC241426
0.569 Remote Similarity NPC150967
0.5688 Remote Similarity NPC215364
0.5684 Remote Similarity NPC151648
0.5673 Remote Similarity NPC476794
0.5673 Remote Similarity NPC171204
0.5673 Remote Similarity NPC97516
0.5673 Remote Similarity NPC65603
0.5673 Remote Similarity NPC476028
0.5673 Remote Similarity NPC470240
0.5673 Remote Similarity NPC141789
0.5673 Remote Similarity NPC41780
0.5673 Remote Similarity NPC187568
0.5667 Remote Similarity NPC476921
0.5667 Remote Similarity NPC75523
0.566 Remote Similarity NPC281132
0.5657 Remote Similarity NPC276290
0.5656 Remote Similarity NPC470072
0.5656 Remote Similarity NPC171734
0.5648 Remote Similarity NPC16488
0.5648 Remote Similarity NPC318468
0.5645 Remote Similarity NPC476875
0.5644 Remote Similarity NPC316185
0.5636 Remote Similarity NPC107787
0.5631 Remote Similarity NPC329852
0.5631 Remote Similarity NPC138408
0.5631 Remote Similarity NPC226669
0.5631 Remote Similarity NPC193351
0.5631 Remote Similarity NPC155587
0.5625 Remote Similarity NPC179087
0.5625 Remote Similarity NPC235625
0.5625 Remote Similarity NPC106791
0.5625 Remote Similarity NPC210303
0.5625 Remote Similarity NPC284656
0.5625 Remote Similarity NPC474658
0.5625 Remote Similarity NPC201889
0.5625 Remote Similarity NPC44343
0.5625 Remote Similarity NPC217940
0.5619 Remote Similarity NPC267231
0.561 Remote Similarity NPC21324
0.5607 Remote Similarity NPC112868
0.5607 Remote Similarity NPC141810
0.5607 Remote Similarity NPC325031
0.56 Remote Similarity NPC265574

  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 NPC474985 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
0.6579 Remote Similarity NPD777 Phase 3
0.6435 Remote Similarity NPD4211 Phase 1
0.621 Remote Similarity NPD2495 Phase 3
0.621 Remote Similarity NPD3159 Discontinued
0.6129 Remote Similarity NPD1773 Discontinued
0.6102 Remote Similarity NPD2147 Approved
0.61 Remote Similarity NPD1452 Discontinued
0.6047 Remote Similarity NPD3677 Clinical (unspecified phase)
0.6032 Remote Similarity NPD2645 Approved
0.6 Remote Similarity NPD2099 Approved
0.5887 Remote Similarity NPD2100 Approved
0.5854 Remote Similarity NPD2090 Approved
0.5814 Remote Similarity NPD1806 Approved
0.5814 Remote Similarity NPD1748 Approved
0.5804 Remote Similarity NPD161 Discontinued
0.5739 Remote Similarity NPD4228 Discovery
0.5738 Remote Similarity NPD6413 Approved
0.5728 Remote Similarity NPD1115 Approved
0.5728 Remote Similarity NPD1114 Approved
0.5703 Remote Similarity NPD4708 Discontinued
0.5682 Remote Similarity NPD2148 Clinical (unspecified phase)
0.568 Remote Similarity NPD1376 Discontinued
0.5659 Remote Similarity NPD806 Approved
0.5659 Remote Similarity NPD805 Approved

  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