Structure

Physi-Chem Properties

Molecular Weight:  395.18
Volume:  391.718
LogP:  2.617
LogD:  1.901
LogS:  -3.968
# Rotatable Bonds:  1
TPSA:  84.86
# H-Bond Aceptor:  6
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.523
Synthetic Accessibility Score:  5.947
Fsp3:  0.7
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:  -4.671
MDCK Permeability:  1.2358035746729001e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.07
Human Intestinal Absorption (HIA):  0.035
20% Bioavailability (F20%):  0.017
30% Bioavailability (F30%):  0.891

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.705
Plasma Protein Binding (PPB):  93.05855560302734%
Volume Distribution (VD):  1.674
Pgp-substrate:  5.023092269897461%

ADMET: Metabolism

CYP1A2-inhibitor:  0.051
CYP1A2-substrate:  0.387
CYP2C19-inhibitor:  0.87
CYP2C19-substrate:  0.532
CYP2C9-inhibitor:  0.789
CYP2C9-substrate:  0.955
CYP2D6-inhibitor:  0.02
CYP2D6-substrate:  0.858
CYP3A4-inhibitor:  0.868
CYP3A4-substrate:  0.263

ADMET: Excretion

Clearance (CL):  5.569
Half-life (T1/2):  0.825

ADMET: Toxicity

hERG Blockers:  0.028
Human Hepatotoxicity (H-HT):  0.924
Drug-inuced Liver Injury (DILI):  0.814
AMES Toxicity:  0.828
Rat Oral Acute Toxicity:  0.043
Maximum Recommended Daily Dose:  0.995
Skin Sensitization:  0.974
Carcinogencity:  0.136
Eye Corrosion:  0.045
Eye Irritation:  0.111
Respiratory Toxicity:  0.947

Download Data

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

  Natural Product: NPC101106

Natural Product ID:  NPC101106
Common Name*:   16-Epi-Latrunculin B
IUPAC Name:   (4S)-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:  NSHPHXHGRHSMIK-WAXGXQFOSA-N
Standard InCHI:  InChI=1S/C20H29NO5S/c1-13-5-3-4-6-14(2)9-18(22)25-16-10-15(8-7-13)26-20(24,11-16)17-12-27-19(23)21-17/h3,5,9,13,15-17,24H,4,6-8,10-12H2,1-2H3,(H,21,23)/b5-3-,14-9-/t13-,15-,16-,17-,20-/m1/s1
SMILES:  C[C@@H]1/C=CCC/C(=CC(=O)O[C@@H]2C[C@@H](CC1)O[C@](C2)([C@H]1CSC(=N1)O)O)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL471071
PubChem CID:   10000783
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]
NPO19376 Cacospongia mycofijiensis Species Thorectidae Eukaryota n.a. n.a. n.a. PMID[18942825]
NPO19376 Cacospongia mycofijiensis Species Thorectidae Eukaryota n.a. Tongan n.a. PMID[19877653]
NPO19376 Cacospongia mycofijiensis Species Thorectidae Eukaryota n.a. n.a. n.a. PMID[22129061]
NPO19376 Cacospongia mycofijiensis Species Thorectidae Eukaryota n.a. n.a. n.a. PMID[30371079]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19376 Cacospongia mycofijiensis Species Thorectidae 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
NPT2657 Cell Line A10 Rattus norvegicus Activity = 5.0 ug ml-1 PMID[509204]
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 38000.0 nM PMID[509205]
NPT400 Cell Line MDA-MB-435 Homo sapiens IC50 = 17000.0 nM PMID[509205]
NPT400 Cell Line MDA-MB-435 Homo sapiens Ratio IC50 = 0.5 n.a. PMID[509205]

☑ 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 NPC101106 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 NPC135216
0.9798 High Similarity NPC287572
0.9798 High Similarity NPC471636
0.97 High Similarity NPC474891
0.9697 High Similarity NPC250187
0.9604 High Similarity NPC127578
0.96 High Similarity NPC474969
0.96 High Similarity NPC476034
0.9417 High Similarity NPC273215
0.9417 High Similarity NPC295444
0.9417 High Similarity NPC268327
0.9417 High Similarity NPC279383
0.9388 High Similarity NPC474873
0.9327 High Similarity NPC475988
0.8972 High Similarity NPC477554
0.8889 High Similarity NPC477553
0.8807 High Similarity NPC477555
0.8519 High Similarity NPC474995
0.8364 Intermediate Similarity NPC474984
0.7442 Intermediate Similarity NPC477557
0.7143 Intermediate Similarity NPC201968
0.7059 Intermediate Similarity NPC477556
0.7009 Intermediate Similarity NPC29501
0.6975 Remote Similarity NPC50694
0.6838 Remote Similarity NPC329305
0.678 Remote Similarity NPC122926
0.678 Remote Similarity NPC113012
0.6696 Remote Similarity NPC4834
0.6667 Remote Similarity NPC175531
0.6607 Remote Similarity NPC475503
0.6549 Remote Similarity NPC475646
0.6496 Remote Similarity NPC477000
0.6496 Remote Similarity NPC477001
0.6496 Remote Similarity NPC75523
0.646 Remote Similarity NPC175614
0.6452 Remote Similarity NPC65045
0.6449 Remote Similarity NPC471494
0.6441 Remote Similarity NPC475918
0.6435 Remote Similarity NPC474985
0.6393 Remote Similarity NPC469865
0.6389 Remote Similarity NPC311163
0.6373 Remote Similarity NPC469880
0.6356 Remote Similarity NPC14537
0.6348 Remote Similarity NPC270813
0.6346 Remote Similarity NPC139712
0.633 Remote Similarity NPC313658
0.633 Remote Similarity NPC316138
0.6325 Remote Similarity NPC473289
0.6303 Remote Similarity NPC473252
0.6303 Remote Similarity NPC472433
0.6281 Remote Similarity NPC24389
0.6281 Remote Similarity NPC473578
0.6261 Remote Similarity NPC476344
0.626 Remote Similarity NPC43648
0.625 Remote Similarity NPC470000
0.625 Remote Similarity NPC474833
0.6241 Remote Similarity NPC477988
0.6231 Remote Similarity NPC326386
0.6231 Remote Similarity NPC477985
0.6231 Remote Similarity NPC471087
0.6228 Remote Similarity NPC150041
0.6214 Remote Similarity NPC477202
0.6207 Remote Similarity NPC234542
0.6198 Remote Similarity NPC475150
0.6186 Remote Similarity NPC477198
0.6183 Remote Similarity NPC329401
0.6183 Remote Similarity NPC477987
0.6182 Remote Similarity NPC199382
0.6168 Remote Similarity NPC471298
0.6154 Remote Similarity NPC293550
0.6154 Remote Similarity NPC323168
0.6154 Remote Similarity NPC473224
0.6154 Remote Similarity NPC111162
0.6154 Remote Similarity NPC477989
0.6154 Remote Similarity NPC477203
0.6154 Remote Similarity NPC477990
0.614 Remote Similarity NPC3568
0.614 Remote Similarity NPC17290
0.614 Remote Similarity NPC192066
0.614 Remote Similarity NPC256570
0.614 Remote Similarity NPC256368
0.6134 Remote Similarity NPC55336
0.6126 Remote Similarity NPC472809
0.6126 Remote Similarity NPC472378
0.6126 Remote Similarity NPC472810
0.6124 Remote Similarity NPC469515
0.6121 Remote Similarity NPC477718
0.6121 Remote Similarity NPC477719
0.6111 Remote Similarity NPC263087
0.6111 Remote Similarity NPC2379
0.6111 Remote Similarity NPC474809
0.6111 Remote Similarity NPC471297
0.6111 Remote Similarity NPC106912
0.6111 Remote Similarity NPC27314
0.6111 Remote Similarity NPC31019
0.6106 Remote Similarity NPC472264
0.6106 Remote Similarity NPC319473
0.6102 Remote Similarity NPC198992
0.609 Remote Similarity NPC477793
0.609 Remote Similarity NPC329919
0.609 Remote Similarity NPC471086
0.6083 Remote Similarity NPC74035
0.6075 Remote Similarity NPC475944
0.6075 Remote Similarity NPC8538
0.6075 Remote Similarity NPC184208
0.6075 Remote Similarity NPC471552
0.6075 Remote Similarity NPC473339
0.6075 Remote Similarity NPC315731
0.6071 Remote Similarity NPC133450
0.6071 Remote Similarity NPC470734
0.6063 Remote Similarity NPC469997
0.6061 Remote Similarity NPC472266
0.6055 Remote Similarity NPC471301
0.6055 Remote Similarity NPC266718
0.6053 Remote Similarity NPC472195
0.6053 Remote Similarity NPC238090
0.6053 Remote Similarity NPC472196
0.6038 Remote Similarity NPC321728
0.6038 Remote Similarity NPC55304
0.6038 Remote Similarity NPC226226
0.6036 Remote Similarity NPC471796
0.6034 Remote Similarity NPC173329
0.6034 Remote Similarity NPC288350
0.6034 Remote Similarity NPC183449
0.6034 Remote Similarity NPC123141
0.6034 Remote Similarity NPC8098
0.6034 Remote Similarity NPC197294
0.6033 Remote Similarity NPC154601
0.6033 Remote Similarity NPC93179
0.6032 Remote Similarity NPC471645
0.6019 Remote Similarity NPC323251
0.6018 Remote Similarity NPC209047
0.6018 Remote Similarity NPC139782
0.6018 Remote Similarity NPC473448
0.6018 Remote Similarity NPC202886
0.6018 Remote Similarity NPC74672
0.6018 Remote Similarity NPC242503
0.6018 Remote Similarity NPC43074
0.6018 Remote Similarity NPC177668
0.6017 Remote Similarity NPC477721
0.6017 Remote Similarity NPC477716
0.6016 Remote Similarity NPC9714
0.6 Remote Similarity NPC67081
0.6 Remote Similarity NPC262312
0.6 Remote Similarity NPC471223
0.6 Remote Similarity NPC474563
0.6 Remote Similarity NPC469895
0.6 Remote Similarity NPC23454
0.6 Remote Similarity NPC70323
0.6 Remote Similarity NPC261750
0.6 Remote Similarity NPC1111
0.6 Remote Similarity NPC35269
0.6 Remote Similarity NPC159698
0.6 Remote Similarity NPC474812
0.5985 Remote Similarity NPC469494
0.5984 Remote Similarity NPC315426
0.5984 Remote Similarity NPC30196
0.5983 Remote Similarity NPC52820
0.5982 Remote Similarity NPC193386
0.5973 Remote Similarity NPC473208
0.5969 Remote Similarity NPC138534
0.5969 Remote Similarity NPC477986
0.5968 Remote Similarity NPC477997
0.5966 Remote Similarity NPC477717
0.5966 Remote Similarity NPC313234
0.5965 Remote Similarity NPC186840
0.5965 Remote Similarity NPC473950
0.5965 Remote Similarity NPC476075
0.5965 Remote Similarity NPC473581
0.5965 Remote Similarity NPC471324
0.5965 Remote Similarity NPC206679
0.5965 Remote Similarity NPC111567
0.5965 Remote Similarity NPC61894
0.5965 Remote Similarity NPC469410
0.5965 Remote Similarity NPC263545
0.5965 Remote Similarity NPC473604
0.5965 Remote Similarity NPC15851
0.5965 Remote Similarity NPC475125
0.5965 Remote Similarity NPC475603
0.5965 Remote Similarity NPC476084
0.5965 Remote Similarity NPC309898
0.5965 Remote Similarity NPC114172
0.5963 Remote Similarity NPC311070
0.5962 Remote Similarity NPC329852
0.5952 Remote Similarity NPC193471
0.5952 Remote Similarity NPC130124
0.595 Remote Similarity NPC44514
0.595 Remote Similarity NPC205176
0.5948 Remote Similarity NPC163365
0.5946 Remote Similarity NPC131813
0.5943 Remote Similarity NPC209135
0.5943 Remote Similarity NPC326753
0.5943 Remote Similarity NPC474816
0.5941 Remote Similarity NPC101622
0.5941 Remote Similarity NPC151481
0.5938 Remote Similarity NPC147707
0.5938 Remote Similarity NPC6531
0.5935 Remote Similarity NPC140251
0.5935 Remote Similarity NPC307903
0.5932 Remote Similarity NPC203627

  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 NPC101106 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
1.0 High Similarity NPD4211 Phase 1
0.6757 Remote Similarity NPD4228 Discovery
0.6721 Remote Similarity NPD7505 Discontinued
0.6417 Remote Similarity NPD6413 Approved
0.6268 Remote Similarity NPD7625 Phase 1
0.6161 Remote Similarity NPD6095 Approved
0.6161 Remote Similarity NPD6094 Approved
0.6098 Remote Similarity NPD6421 Discontinued
0.6018 Remote Similarity NPD8522 Clinical (unspecified phase)
0.6 Remote Similarity NPD6914 Discontinued
0.6 Remote Similarity NPD2258 Approved
0.6 Remote Similarity NPD2259 Approved
0.5968 Remote Similarity NPD6420 Discontinued
0.592 Remote Similarity NPD1719 Phase 1
0.5913 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5909 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5909 Remote Similarity NPD7829 Approved
0.5909 Remote Similarity NPD7830 Approved
0.5909 Remote Similarity NPD7642 Approved
0.5897 Remote Similarity NPD7839 Suspended
0.5891 Remote Similarity NPD7641 Discontinued
0.5877 Remote Similarity NPD6698 Approved
0.5877 Remote Similarity NPD46 Approved
0.5868 Remote Similarity NPD1407 Approved
0.5865 Remote Similarity NPD4480 Approved
0.5821 Remote Similarity NPD8451 Approved
0.5814 Remote Similarity NPD7500 Approved
0.5798 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5794 Remote Similarity NPD2204 Approved
0.5778 Remote Similarity NPD8448 Approved
0.5766 Remote Similarity NPD8392 Approved
0.5766 Remote Similarity NPD8390 Approved
0.5766 Remote Similarity NPD8391 Approved
0.5758 Remote Similarity NPD4209 Clinical (unspecified phase)
0.5758 Remote Similarity NPD8444 Approved
0.5739 Remote Similarity NPD7838 Discovery
0.5714 Remote Similarity NPD8415 Approved
0.5703 Remote Similarity NPD1376 Discontinued
0.569 Remote Similarity NPD4810 Clinical (unspecified phase)
0.568 Remote Similarity NPD6686 Approved
0.5669 Remote Similarity NPD7116 Clinical (unspecified phase)
0.5664 Remote Similarity NPD6422 Discontinued
0.5652 Remote Similarity NPD5370 Suspended
0.563 Remote Similarity NPD3190 Approved
0.563 Remote Similarity NPD3189 Approved
0.563 Remote Similarity NPD8342 Approved
0.563 Remote Similarity NPD8299 Approved
0.563 Remote Similarity NPD3191 Approved
0.563 Remote Similarity NPD8341 Approved
0.563 Remote Similarity NPD8340 Approved
0.5606 Remote Similarity NPD2495 Phase 3

  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