Structure

Physi-Chem Properties

Molecular Weight:  507.3
Volume:  530.086
LogP:  6.574
LogD:  4.558
LogS:  -5.73
# Rotatable Bonds:  9
TPSA:  73.86
# H-Bond Aceptor:  6
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.213
Synthetic Accessibility Score:  6.03
Fsp3:  0.786
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.735
MDCK Permeability:  4.4457148760557175e-05
Pgp-inhibitor:  0.024
Pgp-substrate:  0.09
Human Intestinal Absorption (HIA):  0.021
20% Bioavailability (F20%):  0.977
30% Bioavailability (F30%):  0.418

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.101
Plasma Protein Binding (PPB):  97.9633560180664%
Volume Distribution (VD):  1.67
Pgp-substrate:  1.6184979677200317%

ADMET: Metabolism

CYP1A2-inhibitor:  0.049
CYP1A2-substrate:  0.161
CYP2C19-inhibitor:  0.854
CYP2C19-substrate:  0.179
CYP2C9-inhibitor:  0.906
CYP2C9-substrate:  0.878
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.208
CYP3A4-inhibitor:  0.918
CYP3A4-substrate:  0.288

ADMET: Excretion

Clearance (CL):  10.69
Half-life (T1/2):  0.285

ADMET: Toxicity

hERG Blockers:  0.129
Human Hepatotoxicity (H-HT):  0.948
Drug-inuced Liver Injury (DILI):  0.954
AMES Toxicity:  0.933
Rat Oral Acute Toxicity:  0.033
Maximum Recommended Daily Dose:  0.99
Skin Sensitization:  0.981
Carcinogencity:  0.1
Eye Corrosion:  0.01
Eye Irritation:  0.03
Respiratory Toxicity:  0.965

Download Data

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

  Natural Product: NPC474969

Natural Product ID:  NPC474969
Common Name*:   15-O-Octyllatrunculin B
IUPAC Name:   (4R)-4-[(1R,4S,5Z,9Z,13R,15R)-4,9-dimethyl-15-octoxy-11-oxo-12,16-dioxabicyclo[11.3.1]heptadeca-5,9-dien-15-yl]-1,3-thiazolidin-2-one
Synonyms:  
Standard InCHIKey:  VZIJRUYGPMQTFM-JLQOQYJLSA-N
Standard InCHI:  InChI=1S/C28H45NO5S/c1-4-5-6-7-8-11-16-32-28(25-20-35-27(31)29-25)19-24-18-23(34-28)15-14-21(2)12-9-10-13-22(3)17-26(30)33-24/h9,12,17,21,23-25H,4-8,10-11,13-16,18-20H2,1-3H3,(H,29,31)/b12-9-,22-17-/t21-,23-,24-,25+,28-/m1/s1
SMILES:  CCCCCCCCO[C@]1(O[C@@H]2CC[C@H](C)/C=CCC/C(=CC(=O)O[C@@H](C1)C2)/C)[C@@H]1CSC(=N1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL490517
PubChem CID:   11540713
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
NPT83 Cell Line MCF7 Homo sapiens IC50 = 19952623.15 nM PMID[557203]
NPT314 Organism Bacillus cereus Bacillus cereus MIC = 14700.0 nM PMID[557202]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 14700.0 nM PMID[557202]
NPT20 Organism Candida albicans Candida albicans MIC = 2500.0 nM PMID[557202]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae MIC = 2500.0 nM PMID[557202]

☑ 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 NPC474969 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
1.0 High Similarity NPC476034
0.9899 High Similarity NPC250187
0.96 High Similarity NPC135216
0.96 High Similarity NPC101106
0.951 High Similarity NPC474891
0.9412 High Similarity NPC287572
0.9412 High Similarity NPC471636
0.934 High Similarity NPC477554
0.9333 High Similarity NPC475988
0.9252 High Similarity NPC477553
0.9238 High Similarity NPC268327
0.9238 High Similarity NPC273215
0.9238 High Similarity NPC295444
0.9238 High Similarity NPC279383
0.9231 High Similarity NPC127578
0.9167 High Similarity NPC477555
0.901 High Similarity NPC474873
0.8198 Intermediate Similarity NPC474995
0.8053 Intermediate Similarity NPC474984
0.7734 Intermediate Similarity NPC477557
0.7333 Intermediate Similarity NPC477556
0.7025 Intermediate Similarity NPC201968
0.6891 Remote Similarity NPC29501
0.686 Remote Similarity NPC50694
0.6786 Remote Similarity NPC475503
0.6726 Remote Similarity NPC475646
0.6723 Remote Similarity NPC329305
0.6667 Remote Similarity NPC113012
0.6667 Remote Similarity NPC122926
0.661 Remote Similarity NPC475918
0.6557 Remote Similarity NPC469865
0.6552 Remote Similarity NPC175531
0.6514 Remote Similarity NPC313658
0.6514 Remote Similarity NPC316138
0.6481 Remote Similarity NPC471494
0.648 Remote Similarity NPC65045
0.6446 Remote Similarity NPC473578
0.6435 Remote Similarity NPC4834
0.6423 Remote Similarity NPC43648
0.6415 Remote Similarity NPC471552
0.6415 Remote Similarity NPC473339
0.6391 Remote Similarity NPC477988
0.6387 Remote Similarity NPC477001
0.6387 Remote Similarity NPC477000
0.6387 Remote Similarity NPC75523
0.6381 Remote Similarity NPC139712
0.6364 Remote Similarity NPC475150
0.6356 Remote Similarity NPC477198
0.6348 Remote Similarity NPC175614
0.6336 Remote Similarity NPC477987
0.6336 Remote Similarity NPC329401
0.6325 Remote Similarity NPC474985
0.6316 Remote Similarity NPC192066
0.6316 Remote Similarity NPC256570
0.6316 Remote Similarity NPC17290
0.6316 Remote Similarity NPC3568
0.6316 Remote Similarity NPC256368
0.6303 Remote Similarity NPC55336
0.6296 Remote Similarity NPC31019
0.6296 Remote Similarity NPC263087
0.6296 Remote Similarity NPC27314
0.6296 Remote Similarity NPC2379
0.6296 Remote Similarity NPC106912
0.6286 Remote Similarity NPC474833
0.6279 Remote Similarity NPC470000
0.6273 Remote Similarity NPC311163
0.626 Remote Similarity NPC471087
0.626 Remote Similarity NPC477985
0.626 Remote Similarity NPC326386
0.625 Remote Similarity NPC469880
0.6239 Remote Similarity NPC270813
0.6239 Remote Similarity NPC266718
0.6228 Remote Similarity NPC238090
0.6228 Remote Similarity NPC472195
0.6228 Remote Similarity NPC472196
0.622 Remote Similarity NPC469997
0.6216 Remote Similarity NPC199382
0.6207 Remote Similarity NPC197294
0.6207 Remote Similarity NPC8098
0.6207 Remote Similarity NPC183449
0.6195 Remote Similarity NPC202886
0.6195 Remote Similarity NPC74672
0.6195 Remote Similarity NPC471569
0.6195 Remote Similarity NPC209047
0.6195 Remote Similarity NPC43074
0.6195 Remote Similarity NPC242503
0.6195 Remote Similarity NPC139782
0.619 Remote Similarity NPC477203
0.6186 Remote Similarity NPC477721
0.6186 Remote Similarity NPC477716
0.6183 Remote Similarity NPC477990
0.6183 Remote Similarity NPC477989
0.6183 Remote Similarity NPC323168
0.6183 Remote Similarity NPC293550
0.6183 Remote Similarity NPC111162
0.6179 Remote Similarity NPC24389
0.6174 Remote Similarity NPC35269
0.6174 Remote Similarity NPC23454
0.6174 Remote Similarity NPC262312
0.6174 Remote Similarity NPC70323
0.6174 Remote Similarity NPC477722
0.6174 Remote Similarity NPC159698
0.6172 Remote Similarity NPC9714
0.616 Remote Similarity NPC1111
0.616 Remote Similarity NPC261750
0.6154 Remote Similarity NPC476344
0.6154 Remote Similarity NPC469515
0.6148 Remote Similarity NPC315426
0.6142 Remote Similarity NPC30196
0.614 Remote Similarity NPC61894
0.614 Remote Similarity NPC473581
0.614 Remote Similarity NPC111567
0.614 Remote Similarity NPC263545
0.614 Remote Similarity NPC473604
0.614 Remote Similarity NPC475603
0.614 Remote Similarity NPC186840
0.614 Remote Similarity NPC473950
0.614 Remote Similarity NPC15851
0.614 Remote Similarity NPC309898
0.614 Remote Similarity NPC469410
0.614 Remote Similarity NPC475125
0.6134 Remote Similarity NPC477717
0.6134 Remote Similarity NPC198992
0.6124 Remote Similarity NPC138534
0.6124 Remote Similarity NPC477986
0.6121 Remote Similarity NPC150041
0.6119 Remote Similarity NPC329919
0.6119 Remote Similarity NPC471086
0.6119 Remote Similarity NPC477793
0.6116 Remote Similarity NPC74035
0.6116 Remote Similarity NPC14537
0.6111 Remote Similarity NPC8538
0.6111 Remote Similarity NPC184208
0.6107 Remote Similarity NPC473208
0.6106 Remote Similarity NPC477748
0.6106 Remote Similarity NPC133450
0.6102 Remote Similarity NPC203627
0.61 Remote Similarity NPC472266
0.6095 Remote Similarity NPC477202
0.6094 Remote Similarity NPC6531
0.6083 Remote Similarity NPC473289
0.6078 Remote Similarity NPC163365
0.6068 Remote Similarity NPC173329
0.6068 Remote Similarity NPC45313
0.6068 Remote Similarity NPC288350
0.6066 Remote Similarity NPC201128
0.6066 Remote Similarity NPC472433
0.6066 Remote Similarity NPC473252
0.6066 Remote Similarity NPC239961
0.6063 Remote Similarity NPC471645
0.6061 Remote Similarity NPC316133
0.6061 Remote Similarity NPC315783
0.6061 Remote Similarity NPC318445
0.6058 Remote Similarity NPC477204
0.6055 Remote Similarity NPC471298
0.6053 Remote Similarity NPC477865
0.6053 Remote Similarity NPC477866
0.6053 Remote Similarity NPC177668
0.6048 Remote Similarity NPC133625
0.604 Remote Similarity NPC474812
0.6034 Remote Similarity NPC282088
0.6034 Remote Similarity NPC156782
0.6034 Remote Similarity NPC54961
0.6034 Remote Similarity NPC157353
0.6034 Remote Similarity NPC158445
0.6032 Remote Similarity NPC60432
0.6018 Remote Similarity NPC472378
0.6017 Remote Similarity NPC477719
0.6017 Remote Similarity NPC477718
0.6015 Remote Similarity NPC469494
0.6 Remote Similarity NPC319473
0.6 Remote Similarity NPC471324
0.6 Remote Similarity NPC471297
0.6 Remote Similarity NPC182632
0.6 Remote Similarity NPC282705
0.6 Remote Similarity NPC472264
0.6 Remote Similarity NPC474809
0.6 Remote Similarity NPC114172
0.6 Remote Similarity NPC67917
0.6 Remote Similarity NPC476084
0.6 Remote Similarity NPC206679
0.6 Remote Similarity NPC314268
0.6 Remote Similarity NPC476075
0.6 Remote Similarity NPC477749
0.6 Remote Similarity NPC230889
0.6 Remote Similarity NPC477515
0.6 Remote Similarity NPC313802
0.5985 Remote Similarity NPC469943
0.5985 Remote Similarity NPC316401
0.5984 Remote Similarity NPC205176
0.5981 Remote Similarity NPC326753
0.5966 Remote Similarity NPC234542
0.5963 Remote Similarity NPC469469
0.5963 Remote Similarity NPC475944
0.5963 Remote Similarity NPC315731
0.5962 Remote Similarity NPC327383
0.5962 Remote Similarity NPC185186
0.5962 Remote Similarity NPC477085
0.5952 Remote Similarity NPC58281
0.5948 Remote Similarity NPC159092

  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 NPC474969 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
0.96 High Similarity NPD4211 Phase 1
0.6613 Remote Similarity NPD7505 Discontinued
0.6491 Remote Similarity NPD4228 Discovery
0.6408 Remote Similarity NPD7625 Phase 1
0.6311 Remote Similarity NPD6413 Approved
0.6195 Remote Similarity NPD8522 Clinical (unspecified phase)
0.6148 Remote Similarity NPD6914 Discontinued
0.6129 Remote Similarity NPD6421 Discontinued
0.6061 Remote Similarity NPD7830 Approved
0.6061 Remote Similarity NPD7642 Approved
0.6061 Remote Similarity NPD7829 Approved
0.6053 Remote Similarity NPD6095 Approved
0.6053 Remote Similarity NPD6094 Approved
0.6047 Remote Similarity NPD7641 Discontinued
0.597 Remote Similarity NPD8451 Approved
0.5966 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5926 Remote Similarity NPD8448 Approved
0.5913 Remote Similarity NPD6698 Approved
0.5913 Remote Similarity NPD46 Approved
0.5912 Remote Similarity NPD8391 Approved
0.5912 Remote Similarity NPD8392 Approved
0.5912 Remote Similarity NPD8390 Approved
0.5909 Remote Similarity NPD8444 Approved
0.5902 Remote Similarity NPD2259 Approved
0.5902 Remote Similarity NPD2258 Approved
0.5873 Remote Similarity NPD6420 Discontinued
0.5846 Remote Similarity NPD7500 Approved
0.584 Remote Similarity NPD6686 Approved
0.5812 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5804 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5798 Remote Similarity NPD7839 Suspended
0.5778 Remote Similarity NPD8341 Approved
0.5778 Remote Similarity NPD8340 Approved
0.5778 Remote Similarity NPD8342 Approved
0.5778 Remote Similarity NPD8299 Approved
0.5776 Remote Similarity NPD7838 Discovery
0.5772 Remote Similarity NPD1407 Approved
0.5703 Remote Similarity NPD1719 Phase 1
0.5703 Remote Similarity NPD2204 Approved
0.5702 Remote Similarity NPD6422 Discontinued
0.5662 Remote Similarity NPD4480 Approved
0.5652 Remote Similarity NPD8337 Approved
0.5652 Remote Similarity NPD8336 Approved
0.5634 Remote Similarity NPD8415 Approved
0.563 Remote Similarity NPD8080 Discontinued
0.562 Remote Similarity NPD8273 Phase 1
0.5606 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5603 Remote Similarity NPD8338 Approved
0.56 Remote Similarity NPD7274 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