Structure

Physi-Chem Properties

Molecular Weight:  671.53
Volume:  733.293
LogP:  7.89
LogD:  4.543
LogS:  -3.197
# Rotatable Bonds:  32
TPSA:  148.71
# H-Bond Aceptor:  9
# H-Bond Donor:  6
# Rings:  1
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.036
Synthetic Accessibility Score:  4.329
Fsp3:  0.921
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.425
MDCK Permeability:  9.540462997392751e-06
Pgp-inhibitor:  0.011
Pgp-substrate:  0.672
Human Intestinal Absorption (HIA):  0.392
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.01
Plasma Protein Binding (PPB):  98.7336196899414%
Volume Distribution (VD):  1.032
Pgp-substrate:  2.2607874870300293%

ADMET: Metabolism

CYP1A2-inhibitor:  0.022
CYP1A2-substrate:  0.11
CYP2C19-inhibitor:  0.181
CYP2C19-substrate:  0.042
CYP2C9-inhibitor:  0.074
CYP2C9-substrate:  0.981
CYP2D6-inhibitor:  0.014
CYP2D6-substrate:  0.023
CYP3A4-inhibitor:  0.18
CYP3A4-substrate:  0.006

ADMET: Excretion

Clearance (CL):  2.465
Half-life (T1/2):  0.253

ADMET: Toxicity

hERG Blockers:  0.541
Human Hepatotoxicity (H-HT):  0.111
Drug-inuced Liver Injury (DILI):  0.017
AMES Toxicity:  0.045
Rat Oral Acute Toxicity:  0.034
Maximum Recommended Daily Dose:  0.016
Skin Sensitization:  0.965
Carcinogencity:  0.01
Eye Corrosion:  0.003
Eye Irritation:  0.021
Respiratory Toxicity:  0.534

Download Data

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

  Natural Product: NPC43074

Natural Product ID:  NPC43074
Common Name*:   Turbostatin 3
IUPAC Name:   N-[(E,2S,3R)-3-hydroxy-1-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyhexadec-4-en-2-yl]hexadecanamide
Synonyms:   Turbostatin 3
Standard InCHIKey:  MRQVBTPSVJFXHV-BSUUUAJXSA-N
Standard InCHI:  InChI=1S/C38H73NO8/c1-3-5-7-9-11-13-15-16-18-20-22-24-26-28-34(42)39-31(30-46-38-37(45)36(44)35(43)33(29-40)47-38)32(41)27-25-23-21-19-17-14-12-10-8-6-4-2/h25,27,31-33,35-38,40-41,43-45H,3-24,26,28-30H2,1-2H3,(H,39,42)/b27-25+/t31-,32+,33+,35-,36-,37+,38+/m0/s1
SMILES:  CCCCCCCCCCCCCCCC(=N[C@@H](CO[C@H]1[C@@H]([C@H]([C@H]([C@@H](CO)O1)O)O)O)[C@@H](/C=C/CCCCCCCCCCC)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL505232
PubChem CID:   11787228
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001766] Fatty acyl glycosides
          • [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

*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
NPO23039 Turbo stenogyrus Species Turbinidae Eukaryota n.a. n.a. n.a. PMID[16038534]
NPO23039 Turbo stenogyrus Species Turbinidae 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
NPT168 Cell Line P388 Mus musculus GI50 = 0.25 ug.mL-1 PMID[482530]
NPT83 Cell Line MCF7 Homo sapiens GI50 = 0.48 ug.mL-1 PMID[482530]
NPT395 Cell Line SF-268 Homo sapiens GI50 = 1.9 ug.mL-1 PMID[482530]
NPT397 Cell Line NCI-H460 Homo sapiens GI50 = 0.55 ug.mL-1 PMID[482530]
NPT90 Cell Line DU-145 Homo sapiens GI50 = 2.6 ug.mL-1 PMID[482530]
NPT575 Cell Line KM-20L2 Homo sapiens GI50 = 0.48 ug.mL-1 PMID[482530]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 1.6 ug.mL-1 PMID[482530]

☑ 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 NPC43074 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 NPC242503
1.0 High Similarity NPC139782
1.0 High Similarity NPC74672
1.0 High Similarity NPC209047
0.9882 High Similarity NPC263545
0.9882 High Similarity NPC473950
0.9882 High Similarity NPC473581
0.9882 High Similarity NPC186840
0.9882 High Similarity NPC309898
0.9882 High Similarity NPC475125
0.9882 High Similarity NPC473604
0.9882 High Similarity NPC15851
0.9882 High Similarity NPC111567
0.9655 High Similarity NPC282088
0.9655 High Similarity NPC158445
0.9655 High Similarity NPC256570
0.9655 High Similarity NPC3568
0.9655 High Similarity NPC192066
0.9655 High Similarity NPC17290
0.9655 High Similarity NPC156782
0.9655 High Similarity NPC54961
0.9655 High Similarity NPC157353
0.9651 High Similarity NPC282705
0.9651 High Similarity NPC182632
0.9438 High Similarity NPC8098
0.9438 High Similarity NPC197294
0.9438 High Similarity NPC183449
0.9432 High Similarity NPC70323
0.9432 High Similarity NPC262312
0.9432 High Similarity NPC35269
0.9432 High Similarity NPC23454
0.9222 High Similarity NPC45313
0.9205 High Similarity NPC61894
0.9205 High Similarity NPC475603
0.8469 Intermediate Similarity NPC201128
0.8351 Intermediate Similarity NPC477198
0.7921 Intermediate Similarity NPC475918
0.7882 Intermediate Similarity NPC288086
0.7653 Intermediate Similarity NPC475503
0.7619 Intermediate Similarity NPC103712
0.7619 Intermediate Similarity NPC291196
0.7576 Intermediate Similarity NPC475646
0.7558 Intermediate Similarity NPC55652
0.7419 Intermediate Similarity NPC476523
0.7396 Intermediate Similarity NPC39290
0.7396 Intermediate Similarity NPC159369
0.7386 Intermediate Similarity NPC217095
0.7386 Intermediate Similarity NPC264417
0.7308 Intermediate Similarity NPC74035
0.7222 Intermediate Similarity NPC29501
0.7143 Intermediate Similarity NPC474833
0.7128 Intermediate Similarity NPC228638
0.7097 Intermediate Similarity NPC469469
0.7097 Intermediate Similarity NPC236649
0.7097 Intermediate Similarity NPC21693
0.7083 Intermediate Similarity NPC208473
0.7079 Intermediate Similarity NPC472174
0.7048 Intermediate Similarity NPC55336
0.7043 Intermediate Similarity NPC469943
0.7021 Intermediate Similarity NPC474312
0.6966 Remote Similarity NPC132938
0.6961 Remote Similarity NPC189629
0.6947 Remote Similarity NPC38295
0.6947 Remote Similarity NPC470313
0.6947 Remote Similarity NPC473500
0.6947 Remote Similarity NPC156089
0.6939 Remote Similarity NPC470284
0.6932 Remote Similarity NPC474078
0.6923 Remote Similarity NPC271207
0.6923 Remote Similarity NPC229655
0.6923 Remote Similarity NPC225978
0.6923 Remote Similarity NPC206711
0.6923 Remote Similarity NPC255175
0.6923 Remote Similarity NPC326661
0.6915 Remote Similarity NPC82799
0.6889 Remote Similarity NPC472173
0.6875 Remote Similarity NPC473308
0.6852 Remote Similarity NPC315426
0.6848 Remote Similarity NPC110813
0.6847 Remote Similarity NPC314306
0.6824 Remote Similarity NPC13143
0.6824 Remote Similarity NPC294813
0.6809 Remote Similarity NPC127295
0.6809 Remote Similarity NPC163362
0.6804 Remote Similarity NPC73166
0.68 Remote Similarity NPC477865
0.68 Remote Similarity NPC477866
0.6789 Remote Similarity NPC475150
0.6778 Remote Similarity NPC314678
0.6774 Remote Similarity NPC316807
0.6774 Remote Similarity NPC133377
0.6771 Remote Similarity NPC142111
0.6771 Remote Similarity NPC473315
0.6733 Remote Similarity NPC270005
0.6733 Remote Similarity NPC472199
0.6733 Remote Similarity NPC472197
0.6733 Remote Similarity NPC208537
0.6701 Remote Similarity NPC477199
0.6696 Remote Similarity NPC469865
0.6667 Remote Similarity NPC472196
0.6667 Remote Similarity NPC251026
0.6667 Remote Similarity NPC472195
0.6667 Remote Similarity NPC238090
0.6639 Remote Similarity NPC313342
0.6639 Remote Similarity NPC313333
0.6639 Remote Similarity NPC314512
0.6639 Remote Similarity NPC314451
0.6635 Remote Similarity NPC175614
0.6632 Remote Similarity NPC133226
0.6632 Remote Similarity NPC470147
0.6609 Remote Similarity NPC6531
0.6602 Remote Similarity NPC470283
0.6602 Remote Similarity NPC159698
0.6602 Remote Similarity NPC472198
0.66 Remote Similarity NPC470137
0.6548 Remote Similarity NPC325550
0.6548 Remote Similarity NPC329003
0.6548 Remote Similarity NPC326524
0.6526 Remote Similarity NPC470148
0.6526 Remote Similarity NPC180725
0.6526 Remote Similarity NPC470149
0.6522 Remote Similarity NPC30196
0.6505 Remote Similarity NPC320089
0.65 Remote Similarity NPC118077
0.65 Remote Similarity NPC204639
0.65 Remote Similarity NPC125142
0.65 Remote Similarity NPC475186
0.6496 Remote Similarity NPC314268
0.6496 Remote Similarity NPC67917
0.6496 Remote Similarity NPC313802
0.6496 Remote Similarity NPC477515
0.6475 Remote Similarity NPC477793
0.6475 Remote Similarity NPC329919
0.6471 Remote Similarity NPC473311
0.6458 Remote Similarity NPC100697
0.6458 Remote Similarity NPC471420
0.6452 Remote Similarity NPC3094
0.6444 Remote Similarity NPC327753
0.6444 Remote Similarity NPC327486
0.6444 Remote Similarity NPC223174
0.6436 Remote Similarity NPC248312
0.6429 Remote Similarity NPC321030
0.6429 Remote Similarity NPC473578
0.6423 Remote Similarity NPC313962
0.6421 Remote Similarity NPC248775
0.6415 Remote Similarity NPC240372
0.6408 Remote Similarity NPC302584
0.6408 Remote Similarity NPC469410
0.6404 Remote Similarity NPC268327
0.6404 Remote Similarity NPC261750
0.6404 Remote Similarity NPC1111
0.6404 Remote Similarity NPC273215
0.6404 Remote Similarity NPC279383
0.6404 Remote Similarity NPC295444
0.64 Remote Similarity NPC314361
0.6393 Remote Similarity NPC314282
0.6392 Remote Similarity NPC280367
0.6364 Remote Similarity NPC475035
0.6364 Remote Similarity NPC192025
0.6364 Remote Similarity NPC266718
0.6364 Remote Similarity NPC125253
0.6364 Remote Similarity NPC253975
0.6355 Remote Similarity NPC313440
0.6337 Remote Similarity NPC475037
0.6333 Remote Similarity NPC273185
0.6333 Remote Similarity NPC474812
0.6327 Remote Similarity NPC477390
0.6327 Remote Similarity NPC20072
0.6327 Remote Similarity NPC477385
0.6322 Remote Similarity NPC277570
0.6321 Remote Similarity NPC90583
0.632 Remote Similarity NPC475472
0.6316 Remote Similarity NPC474026
0.6296 Remote Similarity NPC64348
0.6283 Remote Similarity NPC133625
0.6281 Remote Similarity NPC315783
0.6279 Remote Similarity NPC477763
0.6279 Remote Similarity NPC477762
0.6279 Remote Similarity NPC477753
0.6279 Remote Similarity NPC477750
0.6279 Remote Similarity NPC477757
0.6279 Remote Similarity NPC477755
0.627 Remote Similarity NPC73829
0.627 Remote Similarity NPC119794
0.6264 Remote Similarity NPC45060
0.6264 Remote Similarity NPC280065
0.6261 Remote Similarity NPC60432
0.625 Remote Similarity NPC31496
0.625 Remote Similarity NPC150557
0.6239 Remote Similarity NPC471637
0.6239 Remote Similarity NPC154132
0.6239 Remote Similarity NPC475157
0.6239 Remote Similarity NPC475655
0.6239 Remote Similarity NPC57586
0.6239 Remote Similarity NPC2313
0.6239 Remote Similarity NPC154127
0.6238 Remote Similarity NPC470836
0.6237 Remote Similarity NPC305223
0.622 Remote Similarity NPC78189
0.622 Remote Similarity NPC76999

  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 NPC43074 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 NPD8522 Clinical (unspecified phase)
0.7048 Intermediate Similarity NPD1407 Approved
0.6972 Remote Similarity NPD6421 Discontinued
0.6847 Remote Similarity NPD6429 Approved
0.6847 Remote Similarity NPD6430 Approved
0.6639 Remote Similarity NPD8340 Approved
0.6639 Remote Similarity NPD8342 Approved
0.6639 Remote Similarity NPD8299 Approved
0.6639 Remote Similarity NPD8341 Approved
0.6455 Remote Similarity NPD5357 Phase 1
0.6446 Remote Similarity NPD8451 Approved
0.6444 Remote Similarity NPD9445 Approved
0.6393 Remote Similarity NPD8448 Approved
0.6387 Remote Similarity NPD8444 Approved
0.6333 Remote Similarity NPD6436 Phase 3
0.6281 Remote Similarity NPD7830 Approved
0.6281 Remote Similarity NPD7829 Approved
0.6271 Remote Similarity NPD7641 Discontinued
0.624 Remote Similarity NPD8391 Approved
0.624 Remote Similarity NPD8390 Approved
0.624 Remote Similarity NPD8392 Approved
0.6148 Remote Similarity NPD7642 Approved
0.6136 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6058 Remote Similarity NPD3716 Discontinued
0.6019 Remote Similarity NPD4759 Clinical (unspecified phase)
0.6019 Remote Similarity NPD6428 Approved
0.6018 Remote Similarity NPD4211 Phase 1
0.6 Remote Similarity NPD8074 Phase 3
0.5932 Remote Similarity NPD3731 Phase 3
0.5926 Remote Similarity NPD5377 Approved
0.5926 Remote Similarity NPD5378 Approved
0.5926 Remote Similarity NPD5381 Approved
0.5917 Remote Similarity NPD7505 Discontinued
0.5917 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5909 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5877 Remote Similarity NPD6640 Phase 3
0.5872 Remote Similarity NPD7839 Suspended
0.5851 Remote Similarity NPD3212 Clinical (unspecified phase)
0.5841 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5833 Remote Similarity NPD4830 Approved
0.5833 Remote Similarity NPD4831 Approved
0.5833 Remote Similarity NPD4832 Approved
0.581 Remote Similarity NPD618 Clinical (unspecified phase)
0.5794 Remote Similarity NPD7983 Approved
0.5776 Remote Similarity NPD8174 Phase 2
0.5741 Remote Similarity NPD1446 Phase 3
0.5741 Remote Similarity NPD1447 Phase 3
0.5736 Remote Similarity NPD6914 Discontinued
0.5726 Remote Similarity NPD8306 Approved
0.5726 Remote Similarity NPD8305 Approved
0.5726 Remote Similarity NPD6941 Approved
0.5726 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5714 Remote Similarity NPD2269 Approved
0.5701 Remote Similarity NPD3168 Discontinued
0.5701 Remote Similarity NPD6698 Approved
0.5701 Remote Similarity NPD46 Approved
0.5701 Remote Similarity NPD7838 Discovery
0.568 Remote Similarity NPD8080 Discontinued
0.5669 Remote Similarity NPD8273 Phase 1
0.5657 Remote Similarity NPD9435 Approved
0.5657 Remote Similarity NPD9434 Approved
0.5656 Remote Similarity NPD7500 Approved
0.5641 Remote Similarity NPD6686 Approved
0.5639 Remote Similarity NPD8387 Clinical (unspecified phase)
0.563 Remote Similarity NPD8413 Clinical (unspecified phase)
0.563 Remote Similarity NPD7116 Clinical (unspecified phase)
0.5625 Remote Similarity NPD2255 Approved
0.5614 Remote Similarity NPD7141 Clinical (unspecified phase)
0.5614 Remote Similarity NPD7139 Approved
0.5614 Remote Similarity NPD7140 Approved
0.5603 Remote Similarity NPD5376 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