Structure

Physi-Chem Properties

Molecular Weight:  437.19
Volume:  432.464
LogP:  3.4
LogD:  2.46
LogS:  -4.692
# Rotatable Bonds:  2
TPSA:  93.14
# H-Bond Aceptor:  7
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.495
Synthetic Accessibility Score:  6.16
Fsp3:  0.682
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:  -4.799
MDCK Permeability:  6.398215646186145e-06
Pgp-inhibitor:  0.001
Pgp-substrate:  0.035
Human Intestinal Absorption (HIA):  0.085
20% Bioavailability (F20%):  0.755
30% Bioavailability (F30%):  0.962

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.097
Plasma Protein Binding (PPB):  88.48419952392578%
Volume Distribution (VD):  1.267
Pgp-substrate:  9.681453704833984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.017
CYP1A2-substrate:  0.158
CYP2C19-inhibitor:  0.215
CYP2C19-substrate:  0.63
CYP2C9-inhibitor:  0.306
CYP2C9-substrate:  0.519
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.105
CYP3A4-inhibitor:  0.573
CYP3A4-substrate:  0.791

ADMET: Excretion

Clearance (CL):  8.877
Half-life (T1/2):  0.844

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.954
Drug-inuced Liver Injury (DILI):  0.963
AMES Toxicity:  0.869
Rat Oral Acute Toxicity:  0.048
Maximum Recommended Daily Dose:  0.986
Skin Sensitization:  0.972
Carcinogencity:  0.747
Eye Corrosion:  0.023
Eye Irritation:  0.1
Respiratory Toxicity:  0.902

Download Data

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

  Natural Product: NPC474984

Natural Product ID:  NPC474984
Common Name*:   N-Acetyllatrunculin B
IUPAC Name:   (4R)-3-acetyl-4-[(1R,4S,5Z,9Z,13R,15R)-15-hydroxy-4,9-dimethyl-11-oxo-12,16-dioxabicyclo[11.3.1]heptadeca-5,9-dien-15-yl]-1,3-thiazolidin-2-one
Synonyms:  
Standard InCHIKey:  LNEREMNREKXZQC-ITIRMEDBSA-N
Standard InCHI:  InChI=1S/C22H31NO6S/c1-14-6-4-5-7-15(2)10-20(25)28-18-11-17(9-8-14)29-22(27,12-18)19-13-30-21(26)23(19)16(3)24/h4,6,10,14,17-19,27H,5,7-9,11-13H2,1-3H3/b6-4-,15-10-/t14-,17-,18-,19+,22-/m1/s1
SMILES:  CC1CCC2CC(CC(O2)(C3CSC(=O)N3C(=O)C)O)OC(=O)C=C(CCC=C1)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL491161
PubChem CID:   11655045
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 = 232809125.77 nM PMID[483257]
NPT20 Organism Candida albicans Candida albicans MIC = 2500.0 nM PMID[483256]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae MIC = 2500.0 nM PMID[483256]

☑ 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 NPC474984 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
0.9623 High Similarity NPC474995
0.8364 Intermediate Similarity NPC101106
0.8364 Intermediate Similarity NPC135216
0.8214 Intermediate Similarity NPC287572
0.8214 Intermediate Similarity NPC471636
0.8142 Intermediate Similarity NPC474891
0.8125 Intermediate Similarity NPC250187
0.807 Intermediate Similarity NPC127578
0.8053 Intermediate Similarity NPC476034
0.8053 Intermediate Similarity NPC474969
0.8017 Intermediate Similarity NPC475988
0.7931 Intermediate Similarity NPC279383
0.7931 Intermediate Similarity NPC273215
0.7931 Intermediate Similarity NPC295444
0.7931 Intermediate Similarity NPC268327
0.7838 Intermediate Similarity NPC474873
0.7748 Intermediate Similarity NPC474985
0.7583 Intermediate Similarity NPC477554
0.7521 Intermediate Similarity NPC477553
0.7459 Intermediate Similarity NPC477555
0.6723 Remote Similarity NPC473289
0.6694 Remote Similarity NPC58281
0.6693 Remote Similarity NPC65045
0.6639 Remote Similarity NPC188785
0.6612 Remote Similarity NPC477000
0.6612 Remote Similarity NPC477001
0.6593 Remote Similarity NPC477988
0.6591 Remote Similarity NPC326386
0.6591 Remote Similarity NPC471087
0.6591 Remote Similarity NPC477985
0.6544 Remote Similarity NPC120335
0.6541 Remote Similarity NPC329401
0.6541 Remote Similarity NPC477987
0.6515 Remote Similarity NPC323168
0.6515 Remote Similarity NPC293550
0.6515 Remote Similarity NPC477989
0.6515 Remote Similarity NPC111162
0.6515 Remote Similarity NPC477990
0.651 Remote Similarity NPC475342
0.6508 Remote Similarity NPC43648
0.6489 Remote Similarity NPC470000
0.6475 Remote Similarity NPC205176
0.6475 Remote Similarity NPC75523
0.6466 Remote Similarity NPC469999
0.6446 Remote Similarity NPC474244
0.6444 Remote Similarity NPC471086
0.6429 Remote Similarity NPC469455
0.6423 Remote Similarity NPC93179
0.6408 Remote Similarity NPC477557
0.6403 Remote Similarity NPC99864
0.6387 Remote Similarity NPC52820
0.6387 Remote Similarity NPC476344
0.6385 Remote Similarity NPC235625
0.6371 Remote Similarity NPC271562
0.6356 Remote Similarity NPC150041
0.6341 Remote Similarity NPC44514
0.6336 Remote Similarity NPC138534
0.6336 Remote Similarity NPC477986
0.6333 Remote Similarity NPC270813
0.6331 Remote Similarity NPC120420
0.6308 Remote Similarity NPC469997
0.6299 Remote Similarity NPC29501
0.6296 Remote Similarity NPC309525
0.626 Remote Similarity NPC174463
0.6239 Remote Similarity NPC110875
0.6239 Remote Similarity NPC118844
0.6239 Remote Similarity NPC72183
0.6239 Remote Similarity NPC299808
0.621 Remote Similarity NPC469604
0.6202 Remote Similarity NPC193471
0.6202 Remote Similarity NPC130124
0.6195 Remote Similarity NPC475975
0.619 Remote Similarity NPC474099
0.6183 Remote Similarity NPC201968
0.6182 Remote Similarity NPC471768
0.6172 Remote Similarity NPC181510
0.6172 Remote Similarity NPC168758
0.6172 Remote Similarity NPC47857
0.6165 Remote Similarity NPC230849
0.6154 Remote Similarity NPC472536
0.6154 Remote Similarity NPC103391
0.6142 Remote Similarity NPC329305
0.6136 Remote Similarity NPC106791
0.6136 Remote Similarity NPC201889
0.6129 Remote Similarity NPC68001
0.6129 Remote Similarity NPC199831
0.6129 Remote Similarity NPC474827
0.6129 Remote Similarity NPC474828
0.6124 Remote Similarity NPC1111
0.6124 Remote Similarity NPC261750
0.6119 Remote Similarity NPC23963
0.6115 Remote Similarity NPC41162
0.6107 Remote Similarity NPC477556
0.6107 Remote Similarity NPC30196
0.6098 Remote Similarity NPC144714
0.6098 Remote Similarity NPC100810
0.609 Remote Similarity NPC470788
0.6087 Remote Similarity NPC173173
0.608 Remote Similarity NPC64168
0.6068 Remote Similarity NPC81195
0.6063 Remote Similarity NPC171734
0.6061 Remote Similarity NPC6531
0.6047 Remote Similarity NPC316984
0.6047 Remote Similarity NPC30911
0.6047 Remote Similarity NPC476875
0.6034 Remote Similarity NPC324506
0.6031 Remote Similarity NPC50694
0.6029 Remote Similarity NPC318445
0.6029 Remote Similarity NPC316133
0.6017 Remote Similarity NPC17143
0.6017 Remote Similarity NPC47230
0.6015 Remote Similarity NPC17581
0.6015 Remote Similarity NPC470300
0.6015 Remote Similarity NPC284656
0.6015 Remote Similarity NPC476155
0.6 Remote Similarity NPC315188
0.6 Remote Similarity NPC471494
0.6 Remote Similarity NPC173690
0.6 Remote Similarity NPC279833
0.6 Remote Similarity NPC80439
0.6 Remote Similarity NPC60432
0.6 Remote Similarity NPC6271
0.5985 Remote Similarity NPC97580
0.5984 Remote Similarity NPC91036
0.5982 Remote Similarity NPC209232
0.5969 Remote Similarity NPC469603
0.5957 Remote Similarity NPC316401
0.5952 Remote Similarity NPC133420
0.5948 Remote Similarity NPC311163
0.5926 Remote Similarity NPC11379
0.5923 Remote Similarity NPC475608
0.5923 Remote Similarity NPC59249
0.5923 Remote Similarity NPC21713
0.5915 Remote Similarity NPC133089
0.5909 Remote Similarity NPC469880
0.5906 Remote Similarity NPC472856
0.5902 Remote Similarity NPC475503
0.5902 Remote Similarity NPC313821
0.5899 Remote Similarity NPC314282
0.5897 Remote Similarity NPC313658
0.5897 Remote Similarity NPC316138
0.5893 Remote Similarity NPC139712
0.5882 Remote Similarity NPC159568
0.5878 Remote Similarity NPC478024
0.5873 Remote Similarity NPC55336
0.5872 Remote Similarity NPC470994
0.5868 Remote Similarity NPC256368
0.5854 Remote Similarity NPC475646
0.5846 Remote Similarity NPC113012
0.5846 Remote Similarity NPC122926
0.584 Remote Similarity NPC77703
0.5839 Remote Similarity NPC473040
0.5839 Remote Similarity NPC273185
0.5833 Remote Similarity NPC246079
0.5833 Remote Similarity NPC469597
0.5826 Remote Similarity NPC106912
0.5826 Remote Similarity NPC27314
0.5826 Remote Similarity NPC2379
0.5826 Remote Similarity NPC263087
0.5826 Remote Similarity NPC31019
0.5798 Remote Similarity NPC133450
0.5797 Remote Similarity NPC314629
0.5793 Remote Similarity NPC82129
0.5789 Remote Similarity NPC277341
0.5789 Remote Similarity NPC471552
0.5789 Remote Similarity NPC473339
0.5789 Remote Similarity NPC226982
0.5781 Remote Similarity NPC475918
0.5781 Remote Similarity NPC472433
0.5772 Remote Similarity NPC175614
0.5766 Remote Similarity NPC477202
0.5763 Remote Similarity NPC199382
0.576 Remote Similarity NPC26597
0.5758 Remote Similarity NPC314550
0.5758 Remote Similarity NPC469865
0.5755 Remote Similarity NPC314451
0.5755 Remote Similarity NPC313333
0.5755 Remote Similarity NPC313342
0.5755 Remote Similarity NPC314512
0.575 Remote Similarity NPC177668
0.575 Remote Similarity NPC53240
0.5748 Remote Similarity NPC476877
0.5736 Remote Similarity NPC315426
0.5726 Remote Similarity NPC4834
0.5726 Remote Similarity NPC319913
0.5724 Remote Similarity NPC471256
0.5714 Remote Similarity NPC283783
0.5714 Remote Similarity NPC477203
0.5714 Remote Similarity NPC175531
0.5704 Remote Similarity NPC475642
0.5704 Remote Similarity NPC316205
0.5704 Remote Similarity NPC315387
0.5702 Remote Similarity NPC145707
0.5692 Remote Similarity NPC207820
0.5692 Remote Similarity NPC470072
0.5692 Remote Similarity NPC476276
0.5691 Remote Similarity NPC471635
0.5691 Remote Similarity NPC25033
0.5691 Remote Similarity NPC476261
0.5691 Remote Similarity NPC470382

  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 NPC474984 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
0.8364 Intermediate Similarity NPD4211 Phase 1
0.6403 Remote Similarity NPD8415 Approved
0.6336 Remote Similarity NPD2495 Phase 3
0.629 Remote Similarity NPD777 Phase 3
0.6241 Remote Similarity NPD8387 Clinical (unspecified phase)
0.6202 Remote Similarity NPD1376 Discontinued
0.6176 Remote Similarity NPD3677 Clinical (unspecified phase)
0.6136 Remote Similarity NPD1773 Discontinued
0.609 Remote Similarity NPD3159 Discontinued
0.6058 Remote Similarity NPD8273 Phase 1
0.6047 Remote Similarity NPD2204 Approved
0.6033 Remote Similarity NPD4228 Discovery
0.6029 Remote Similarity NPD7642 Approved
0.6027 Remote Similarity NPD8384 Approved
0.6015 Remote Similarity NPD7641 Discontinued
0.5942 Remote Similarity NPD8451 Approved
0.5926 Remote Similarity NPD2645 Approved
0.5902 Remote Similarity NPD3189 Approved
0.5902 Remote Similarity NPD3190 Approved
0.5902 Remote Similarity NPD3191 Approved
0.5899 Remote Similarity NPD8448 Approved
0.5887 Remote Similarity NPD8391 Approved
0.5887 Remote Similarity NPD8392 Approved
0.5887 Remote Similarity NPD8390 Approved
0.5859 Remote Similarity NPD2147 Approved
0.5852 Remote Similarity NPD7519 Approved
0.5852 Remote Similarity NPD7517 Approved
0.5852 Remote Similarity NPD7518 Approved
0.5833 Remote Similarity NPD8414 Discontinued
0.5821 Remote Similarity NPD7505 Discontinued
0.5786 Remote Similarity NPD4557 Approved
0.5778 Remote Similarity NPD2099 Approved
0.5769 Remote Similarity NPD6413 Approved
0.5755 Remote Similarity NPD8299 Approved
0.5755 Remote Similarity NPD8341 Approved
0.5755 Remote Similarity NPD8340 Approved
0.5755 Remote Similarity NPD8342 Approved
0.5725 Remote Similarity NPD1806 Approved
0.5725 Remote Similarity NPD1748 Approved
0.5705 Remote Similarity NPD3480 Approved
0.5694 Remote Similarity NPD4125 Approved
0.5672 Remote Similarity NPD2100 Approved
0.5669 Remote Similarity NPD4648 Approved
0.5669 Remote Similarity NPD4646 Approved
0.5669 Remote Similarity NPD4647 Approved
0.5664 Remote Similarity NPD7751 Phase 1
0.5658 Remote Similarity NPD5265 Approved
0.5658 Remote Similarity NPD5264 Approved
0.5645 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5639 Remote Similarity NPD2090 Approved
0.5621 Remote Similarity NPD7625 Phase 1
0.5603 Remote Similarity NPD2148 Clinical (unspecified phase)
0.56 Remote Similarity NPD3648 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