Structure

Physi-Chem Properties

Molecular Weight:  681.46
Volume:  718.939
LogP:  4.859
LogD:  3.215
LogS:  -4.337
# Rotatable Bonds:  11
TPSA:  139.83
# H-Bond Aceptor:  12
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.226
Synthetic Accessibility Score:  5.359
Fsp3:  0.833
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
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:  -5.063
MDCK Permeability:  2.0487619622144848e-05
Pgp-inhibitor:  1.0
Pgp-substrate:  0.029
Human Intestinal Absorption (HIA):  0.289
20% Bioavailability (F20%):  0.013
30% Bioavailability (F30%):  0.564

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.017
Plasma Protein Binding (PPB):  93.59265899658203%
Volume Distribution (VD):  1.301
Pgp-substrate:  2.161306381225586%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.096
CYP2C19-inhibitor:  0.109
CYP2C19-substrate:  0.942
CYP2C9-inhibitor:  0.138
CYP2C9-substrate:  0.088
CYP2D6-inhibitor:  0.072
CYP2D6-substrate:  0.087
CYP3A4-inhibitor:  0.695
CYP3A4-substrate:  0.913

ADMET: Excretion

Clearance (CL):  5.352
Half-life (T1/2):  0.04

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.987
Drug-inuced Liver Injury (DILI):  0.98
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.022
Maximum Recommended Daily Dose:  0.011
Skin Sensitization:  0.032
Carcinogencity:  0.002
Eye Corrosion:  0.003
Eye Irritation:  0.005
Respiratory Toxicity:  0.007

Download Data

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

  Natural Product: NPC477145

Natural Product ID:  NPC477145
Common Name*:   (3S,6R,9S,12R,15S,18R)-3,9-dibutyl-6,12,18-triisopropyl-4,10,16-trimethyl-15-sec-butyl-1,7,13-trioxa-4,10,16-triazacyclooctadecane-2,5,8,11,14,17-hexone
IUPAC Name:   (3S,6R,9S,12R,15S,18R)-3-butan-2-yl-9,15-dibutyl-4,10,16-trimethyl-6,12,18-tri(propan-2-yl)-1,7,13-trioxa-4,10,16-triazacyclooctadecane-2,5,8,11,14,17-hexone
Synonyms:  
Standard InCHIKey:  GVDAJJRPXXFXKC-PTXBXGOCSA-N
Standard InCHI:  InChI=1S/C36H63N3O9/c1-14-17-19-25-34(43)46-28(21(4)5)31(40)37(11)26(20-18-15-2)35(44)47-30(23(8)9)33(42)39(13)27(24(10)16-3)36(45)48-29(22(6)7)32(41)38(25)12/h21-30H,14-20H2,1-13H3/t24?,25-,26-,27-,28+,29+,30+/m0/s1
SMILES:  CCCC[C@H]1C(=O)O[C@@H](C(=O)N([C@H](C(=O)O[C@@H](C(=O)N([C@H](C(=O)O[C@@H](C(=O)N1C)C(C)C)CCCC)C)C(C)C)C(C)CC)C)C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   16727691
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0001813] Peptidomimetics
        • [CHEMONTID:0001961] Depsipeptides
          • [CHEMONTID:0001994] Cyclic depsipeptides

*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
NPO29266 Fusarium oxysporum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[16562855]
NPO29266 Fusarium oxysporum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[17286429]
NPO29266 Fusarium oxysporum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[9014349]
NPO29266 Fusarium oxysporum Species Nectriaceae 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
NPT20 Organism Candida albicans Candida albicans IC50 = 2 ug/ml PMID[16562855]
NPT20 Organism Candida albicans Candida albicans MIC = 3.13 ug/ml PMID[16562855]
NPT85 Organism Filobasidiella neoformans Cryptococcus neoformans IC50 = 3.5 ug/ml PMID[16562855]
NPT86 Organism Mycobacterium intracellulare Mycobacterium intracellulare IC50 = 5 ug/ml PMID[16562855]
NPT85 Organism Filobasidiella neoformans Cryptococcus neoformans MIC = 12.5 ug/ml PMID[16562855]
NPT86 Organism Mycobacterium intracellulare Mycobacterium intracellulare MIC = 50 ug/ml PMID[16562855]

☑ 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 NPC477145 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 NPC473741
0.9437 High Similarity NPC178919
0.9167 High Similarity NPC263281
0.8873 High Similarity NPC29598
0.8873 High Similarity NPC212866
0.8732 High Similarity NPC10716
0.7614 Intermediate Similarity NPC476019
0.7609 Intermediate Similarity NPC220234
0.759 Intermediate Similarity NPC246005
0.7368 Intermediate Similarity NPC5864
0.7368 Intermediate Similarity NPC301148
0.7368 Intermediate Similarity NPC124554
0.7333 Intermediate Similarity NPC173763
0.7333 Intermediate Similarity NPC62263
0.7333 Intermediate Similarity NPC471098
0.7222 Intermediate Similarity NPC474576
0.7216 Intermediate Similarity NPC124549
0.7216 Intermediate Similarity NPC323720
0.7191 Intermediate Similarity NPC322966
0.7113 Intermediate Similarity NPC198344
0.7111 Intermediate Similarity NPC474593
0.7111 Intermediate Similarity NPC475801
0.7 Intermediate Similarity NPC171734
0.7 Intermediate Similarity NPC67009
0.6875 Remote Similarity NPC475440
0.6667 Remote Similarity NPC471097
0.6667 Remote Similarity NPC475149
0.6634 Remote Similarity NPC475637
0.6591 Remote Similarity NPC53858
0.6591 Remote Similarity NPC84128
0.6465 Remote Similarity NPC13175
0.6465 Remote Similarity NPC475791
0.6463 Remote Similarity NPC478256
0.6421 Remote Similarity NPC315237
0.6375 Remote Similarity NPC325117
0.6375 Remote Similarity NPC322319
0.6375 Remote Similarity NPC326651
0.6364 Remote Similarity NPC475758
0.625 Remote Similarity NPC477238
0.6235 Remote Similarity NPC208657
0.6163 Remote Similarity NPC86064
0.6162 Remote Similarity NPC473597
0.6146 Remote Similarity NPC477538
0.6136 Remote Similarity NPC233108
0.6118 Remote Similarity NPC141325
0.6087 Remote Similarity NPC472351
0.6078 Remote Similarity NPC188785
0.6071 Remote Similarity NPC477237
0.6055 Remote Similarity NPC471202
0.6055 Remote Similarity NPC63191
0.6049 Remote Similarity NPC472609
0.6047 Remote Similarity NPC138435
0.6047 Remote Similarity NPC43219
0.6 Remote Similarity NPC103391
0.6 Remote Similarity NPC476243
0.6 Remote Similarity NPC47076
0.6 Remote Similarity NPC134504
0.6 Remote Similarity NPC476156
0.6 Remote Similarity NPC476117
0.6 Remote Similarity NPC216090
0.6 Remote Similarity NPC472536
0.6 Remote Similarity NPC476137
0.5978 Remote Similarity NPC235078
0.5977 Remote Similarity NPC327272
0.5966 Remote Similarity NPC239990
0.5966 Remote Similarity NPC105114
0.5966 Remote Similarity NPC89923
0.5966 Remote Similarity NPC71933
0.5966 Remote Similarity NPC152850
0.5952 Remote Similarity NPC320663
0.5952 Remote Similarity NPC224700
0.5934 Remote Similarity NPC23984
0.5934 Remote Similarity NPC476302
0.5914 Remote Similarity NPC155670
0.5914 Remote Similarity NPC95478
0.5914 Remote Similarity NPC145748
0.5909 Remote Similarity NPC476130
0.5909 Remote Similarity NPC476324
0.5889 Remote Similarity NPC31756
0.5882 Remote Similarity NPC476291
0.5882 Remote Similarity NPC136453
0.5851 Remote Similarity NPC227051
0.5842 Remote Similarity NPC471843
0.5833 Remote Similarity NPC52533
0.582 Remote Similarity NPC157311
0.5806 Remote Similarity NPC47135
0.5772 Remote Similarity NPC8761
0.5772 Remote Similarity NPC44805
0.5769 Remote Similarity NPC278209
0.5766 Remote Similarity NPC469597
0.5765 Remote Similarity NPC193280
0.5765 Remote Similarity NPC314273
0.5763 Remote Similarity NPC309525
0.5727 Remote Similarity NPC476875
0.5714 Remote Similarity NPC477729
0.5714 Remote Similarity NPC178632
0.5714 Remote Similarity NPC315535
0.5714 Remote Similarity NPC478017
0.5714 Remote Similarity NPC315131
0.5701 Remote Similarity NPC241394
0.5698 Remote Similarity NPC476285
0.5691 Remote Similarity NPC120420
0.5682 Remote Similarity NPC476248
0.5658 Remote Similarity NPC325180
0.5658 Remote Similarity NPC35816
0.5657 Remote Similarity NPC47230
0.5657 Remote Similarity NPC17143
0.5652 Remote Similarity NPC474702
0.5648 Remote Similarity NPC137453
0.5645 Remote Similarity NPC99864
0.5625 Remote Similarity NPC319991
0.5607 Remote Similarity NPC128303
0.5607 Remote Similarity NPC205176
0.5604 Remote Similarity NPC316242

  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 NPC477145 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
0.8873 High Similarity NPD7840 Approved
0.6706 Remote Similarity NPD8143 Approved
0.6706 Remote Similarity NPD8144 Approved
0.6667 Remote Similarity NPD2696 Approved
0.6667 Remote Similarity NPD2697 Approved
0.6667 Remote Similarity NPD2695 Approved
0.6667 Remote Similarity NPD2694 Approved
0.6598 Remote Similarity NPD3715 Approved
0.6598 Remote Similarity NPD3713 Approved
0.6598 Remote Similarity NPD3714 Approved
0.6506 Remote Similarity NPD6704 Discontinued
0.6486 Remote Similarity NPD4281 Clinical (unspecified phase)
0.6265 Remote Similarity NPD2220 Clinical (unspecified phase)
0.6146 Remote Similarity NPD4780 Clinical (unspecified phase)
0.6071 Remote Similarity NPD3726 Approved
0.6071 Remote Similarity NPD3725 Approved
0.6019 Remote Similarity NPD8300 Approved
0.6019 Remote Similarity NPD8301 Approved
0.6 Remote Similarity NPD7535 Discontinued
0.5979 Remote Similarity NPD2682 Approved
0.5957 Remote Similarity NPD7760 Phase 2
0.5957 Remote Similarity NPD7759 Phase 2
0.5952 Remote Similarity NPD3724 Clinical (unspecified phase)
0.5952 Remote Similarity NPD8278 Approved
0.5909 Remote Similarity NPD11 Approved
0.5909 Remote Similarity NPD376 Approved
0.59 Remote Similarity NPD7841 Clinical (unspecified phase)
0.5882 Remote Similarity NPD8277 Approved
0.5816 Remote Similarity NPD4261 Phase 1
0.5806 Remote Similarity NPD7345 Approved
0.5789 Remote Similarity NPD3723 Clinical (unspecified phase)
0.5784 Remote Similarity NPD8038 Phase 2
0.5765 Remote Similarity NPD620 Approved
0.5761 Remote Similarity NPD612 Discontinued
0.5761 Remote Similarity NPD7763 Phase 2
0.5761 Remote Similarity NPD7762 Phase 2
0.5758 Remote Similarity NPD6699 Clinical (unspecified phase)
0.5714 Remote Similarity NPD7917 Clinical (unspecified phase)
0.5714 Remote Similarity NPD7918 Clinical (unspecified phase)
0.5698 Remote Similarity NPD9649 Approved
0.5682 Remote Similarity NPD355 Phase 2
0.5663 Remote Similarity NPD9648 Approved
0.5663 Remote Similarity NPD4272 Discontinued
0.5658 Remote Similarity NPD9660 Approved
0.5648 Remote Similarity NPD8140 Approved
0.5645 Remote Similarity NPD8415 Approved
0.5604 Remote Similarity NPD3160 Suspended
0.56 Remote Similarity NPD8387 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