Structure

Physi-Chem Properties

Molecular Weight:  465.32
Volume:  487.293
LogP:  2.04
LogD:  0.928
LogS:  0.378
# Rotatable Bonds:  20
TPSA:  95.89
# H-Bond Aceptor:  7
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.134
Synthetic Accessibility Score:  4.14
Fsp3:  0.957
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.465
MDCK Permeability:  8.52080192998983e-05
Pgp-inhibitor:  0.009
Pgp-substrate:  0.366
Human Intestinal Absorption (HIA):  0.362
20% Bioavailability (F20%):  0.983
30% Bioavailability (F30%):  0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.019
Plasma Protein Binding (PPB):  77.44329071044922%
Volume Distribution (VD):  0.57
Pgp-substrate:  36.69559097290039%

ADMET: Metabolism

CYP1A2-inhibitor:  0.02
CYP1A2-substrate:  0.732
CYP2C19-inhibitor:  0.049
CYP2C19-substrate:  0.149
CYP2C9-inhibitor:  0.021
CYP2C9-substrate:  0.765
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.861
CYP3A4-inhibitor:  0.444
CYP3A4-substrate:  0.066

ADMET: Excretion

Clearance (CL):  3.574
Half-life (T1/2):  0.864

ADMET: Toxicity

hERG Blockers:  0.259
Human Hepatotoxicity (H-HT):  0.195
Drug-inuced Liver Injury (DILI):  0.009
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.03
Maximum Recommended Daily Dose:  0.943
Skin Sensitization:  0.502
Carcinogencity:  0.171
Eye Corrosion:  0.004
Eye Irritation:  0.011
Respiratory Toxicity:  0.41

Download Data

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

  Natural Product: NPC330017

Natural Product ID:  NPC330017
Common Name*:   Stellettacholine B
IUPAC Name:   [(2R)-3-(2,12-dimethyltridecanoyloxy)-2-hydroxypropoxy]-[2-(trimethylazaniumyl)ethyl]phosphinate
Synonyms:   Stellettacholine B
Standard InCHIKey:  XZVWVQIWDKJIQE-FOIFJWKZSA-N
Standard InCHI:  InChI=1S/C23H48NO6P/c1-20(2)14-12-10-8-7-9-11-13-15-21(3)23(26)29-18-22(25)19-30-31(27,28)17-16-24(4,5)6/h20-22,25H,7-19H2,1-6H3/t21?,22-/m1/s1
SMILES:  O[C@@H](COP(=O)(CC[N+](C)(C)C)[O-])COC(=O)C(CCCCCCCCCC(C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2021365
PubChem CID:   44584544
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003616] Glycerophosphonolipids
        • [CHEMONTID:0003620] Glycerophosphonocholines
          • [CHEMONTID:0003617] Glycerol-3-phosphonocholines

*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
NPO33189 Stelletta sp. Species Ancorinidae Eukaryota n.a. n.a. n.a. PMID[10479342]
NPO33189 Stelletta sp. Species Ancorinidae Eukaryota n.a. (20 m depth) off Ullung Island, Korea 2001-OCT PMID[12662102]
NPO33189 Stelletta sp. Species Ancorinidae Eukaryota n.a. n.a. n.a. PMID[12713419]
NPO33189 Stelletta sp. Species Ancorinidae Eukaryota n.a. n.a. n.a. PMID[12762820]
NPO33189 Stelletta sp. Species Ancorinidae Eukaryota n.a. n.a. n.a. PMID[23465061]
NPO33189 Stelletta sp. Species Ancorinidae Eukaryota n.a. n.a. n.a. PMID[31646862]
NPO33189 Stelletta sp. Species Ancorinidae Eukaryota n.a. n.a. n.a. PMID[8946745]
NPO33189 Stelletta sp. Species Ancorinidae Eukaryota n.a. n.a. n.a. PMID[9296951]

☑ 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
NPT146 Cell Line SK-OV-3 Homo sapiens ED50 = 4.8 ug ml-1 PMID[456159]
NPT147 Cell Line SK-MEL-2 Homo sapiens ED50 = 6.3 ug ml-1 PMID[456159]
NPT81 Cell Line A549 Homo sapiens ED50 = 7.4 ug ml-1 PMID[456159]
NPT574 Cell Line XF498 Homo sapiens ED50 = 24.1 ug ml-1 PMID[456159]
NPT148 Cell Line HCT-15 Homo sapiens ED50 = 26.9 ug ml-1 PMID[456159]

☑ 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 NPC330017 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
0.9067 High Similarity NPC474702
0.875 High Similarity NPC324165
0.875 High Similarity NPC126366
0.875 High Similarity NPC170963
0.875 High Similarity NPC114640
0.875 High Similarity NPC33267
0.875 High Similarity NPC169976
0.8378 Intermediate Similarity NPC54460
0.8056 Intermediate Similarity NPC238646
0.8 Intermediate Similarity NPC470268
0.7973 Intermediate Similarity NPC320663
0.7973 Intermediate Similarity NPC224700
0.7606 Intermediate Similarity NPC470363
0.75 Intermediate Similarity NPC178758
0.75 Intermediate Similarity NPC196102
0.7416 Intermediate Similarity NPC329906
0.7361 Intermediate Similarity NPC201338
0.7361 Intermediate Similarity NPC474627
0.7361 Intermediate Similarity NPC328786
0.6905 Remote Similarity NPC473984
0.6901 Remote Similarity NPC23155
0.6901 Remote Similarity NPC469937
0.6901 Remote Similarity NPC53463
0.6901 Remote Similarity NPC320588
0.6875 Remote Similarity NPC321873
0.6709 Remote Similarity NPC469925
0.6625 Remote Similarity NPC82315
0.6588 Remote Similarity NPC325936
0.6538 Remote Similarity NPC314103
0.65 Remote Similarity NPC286842
0.6456 Remote Similarity NPC322319
0.6456 Remote Similarity NPC326651
0.6456 Remote Similarity NPC325117
0.6429 Remote Similarity NPC26253
0.641 Remote Similarity NPC235788
0.6404 Remote Similarity NPC47135
0.6386 Remote Similarity NPC474403
0.6353 Remote Similarity NPC228411
0.6338 Remote Similarity NPC55678
0.631 Remote Similarity NPC305223
0.631 Remote Similarity NPC474100
0.631 Remote Similarity NPC51249
0.631 Remote Similarity NPC475232
0.631 Remote Similarity NPC473775
0.631 Remote Similarity NPC475260
0.631 Remote Similarity NPC473699
0.625 Remote Similarity NPC476330
0.6207 Remote Similarity NPC316242
0.6154 Remote Similarity NPC320936
0.6143 Remote Similarity NPC249754
0.6136 Remote Similarity NPC478017
0.6136 Remote Similarity NPC315131
0.6136 Remote Similarity NPC315535
0.6118 Remote Similarity NPC43219
0.6078 Remote Similarity NPC227622
0.6056 Remote Similarity NPC106872
0.6049 Remote Similarity NPC469926
0.6047 Remote Similarity NPC86064
0.6042 Remote Similarity NPC476019
0.6027 Remote Similarity NPC287811
0.6027 Remote Similarity NPC314084
0.6026 Remote Similarity NPC472020
0.6026 Remote Similarity NPC472019
0.6026 Remote Similarity NPC226602
0.6024 Remote Similarity NPC273508
0.6024 Remote Similarity NPC209327
0.6023 Remote Similarity NPC474003
0.6023 Remote Similarity NPC233108
0.6 Remote Similarity NPC184550
0.6 Remote Similarity NPC322966
0.6 Remote Similarity NPC185419
0.6 Remote Similarity NPC474552
0.5957 Remote Similarity NPC477728
0.5955 Remote Similarity NPC218817
0.5955 Remote Similarity NPC475616
0.5955 Remote Similarity NPC11796
0.5952 Remote Similarity NPC28526
0.5952 Remote Similarity NPC127145
0.5952 Remote Similarity NPC475930
0.5952 Remote Similarity NPC476285
0.5949 Remote Similarity NPC472021
0.593 Remote Similarity NPC308096
0.593 Remote Similarity NPC291228
0.5915 Remote Similarity NPC328497
0.5915 Remote Similarity NPC21844
0.5915 Remote Similarity NPC324004
0.5914 Remote Similarity NPC277918
0.5904 Remote Similarity NPC104537
0.5904 Remote Similarity NPC473829
0.5904 Remote Similarity NPC127091
0.5904 Remote Similarity NPC330426
0.5904 Remote Similarity NPC22101
0.5904 Remote Similarity NPC475443
0.5904 Remote Similarity NPC271921
0.5904 Remote Similarity NPC206601
0.5904 Remote Similarity NPC148192
0.589 Remote Similarity NPC90904
0.5889 Remote Similarity NPC216090
0.5882 Remote Similarity NPC474674
0.5857 Remote Similarity NPC287231
0.5857 Remote Similarity NPC47363
0.5854 Remote Similarity NPC474402
0.5849 Remote Similarity NPC137453
0.5833 Remote Similarity NPC324981
0.5833 Remote Similarity NPC324793
0.5833 Remote Similarity NPC48218
0.5833 Remote Similarity NPC473559
0.5833 Remote Similarity NPC141481
0.5833 Remote Similarity NPC477878
0.5824 Remote Similarity NPC103634
0.5823 Remote Similarity NPC475821
0.5811 Remote Similarity NPC100096
0.5789 Remote Similarity NPC289979
0.5783 Remote Similarity NPC315525
0.5783 Remote Similarity NPC135043
0.5778 Remote Similarity NPC470014
0.5775 Remote Similarity NPC30195
0.5775 Remote Similarity NPC12438
0.5775 Remote Similarity NPC308301
0.5765 Remote Similarity NPC476291
0.5765 Remote Similarity NPC285003
0.5765 Remote Similarity NPC473772
0.5765 Remote Similarity NPC478256
0.5765 Remote Similarity NPC137620
0.5765 Remote Similarity NPC241265
0.5765 Remote Similarity NPC474675
0.5755 Remote Similarity NPC471844
0.5745 Remote Similarity NPC227051
0.573 Remote Similarity NPC474020
0.5714 Remote Similarity NPC294748
0.5714 Remote Similarity NPC85759
0.5714 Remote Similarity NPC146992
0.5714 Remote Similarity NPC477344
0.5714 Remote Similarity NPC22742
0.5714 Remote Similarity NPC158302
0.5714 Remote Similarity NPC477346
0.5699 Remote Similarity NPC100366
0.5699 Remote Similarity NPC311642
0.5699 Remote Similarity NPC242771
0.5699 Remote Similarity NPC164289
0.5699 Remote Similarity NPC477730
0.5698 Remote Similarity NPC476660
0.5684 Remote Similarity NPC83839
0.5684 Remote Similarity NPC476715
0.5679 Remote Similarity NPC469923
0.5676 Remote Similarity NPC305182
0.567 Remote Similarity NPC203170
0.5667 Remote Similarity NPC83108
0.5667 Remote Similarity NPC214030
0.5663 Remote Similarity NPC306805
0.5663 Remote Similarity NPC215987
0.5658 Remote Similarity NPC72722
0.5652 Remote Similarity NPC200446
0.5647 Remote Similarity NPC474298
0.5647 Remote Similarity NPC474299
0.5647 Remote Similarity NPC473985
0.5647 Remote Similarity NPC97736
0.5647 Remote Similarity NPC50228
0.5647 Remote Similarity NPC319007
0.5647 Remote Similarity NPC28348
0.5647 Remote Similarity NPC475808
0.5638 Remote Similarity NPC259173
0.5638 Remote Similarity NPC145748
0.5638 Remote Similarity NPC95478
0.5638 Remote Similarity NPC155670
0.5634 Remote Similarity NPC55023
0.5625 Remote Similarity NPC469924
0.5625 Remote Similarity NPC92139
0.5625 Remote Similarity NPC319131
0.5625 Remote Similarity NPC174485
0.5618 Remote Similarity NPC476130
0.5618 Remote Similarity NPC81052
0.5618 Remote Similarity NPC476324
0.5618 Remote Similarity NPC217725
0.5616 Remote Similarity NPC200618
0.5616 Remote Similarity NPC131770
0.5612 Remote Similarity NPC39290
0.5612 Remote Similarity NPC159369
0.5612 Remote Similarity NPC477729
0.561 Remote Similarity NPC325773
0.5604 Remote Similarity NPC252483
0.5604 Remote Similarity NPC191345

  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 NPC330017 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
0.8108 Intermediate Similarity NPD8277 Approved
0.7973 Intermediate Similarity NPD8278 Approved
0.6901 Remote Similarity NPD3728 Approved
0.6901 Remote Similarity NPD3730 Approved
0.6806 Remote Similarity NPD6950 Discontinued
0.6711 Remote Similarity NPD4283 Discontinued
0.6623 Remote Similarity NPD7347 Clinical (unspecified phase)
0.6438 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6404 Remote Similarity NPD7345 Approved
0.6341 Remote Similarity NPD3725 Approved
0.6341 Remote Similarity NPD3726 Approved
0.6329 Remote Similarity NPD7909 Approved
0.6286 Remote Similarity NPD6125 Clinical (unspecified phase)
0.6136 Remote Similarity NPD7917 Clinical (unspecified phase)
0.6136 Remote Similarity NPD7918 Clinical (unspecified phase)
0.6078 Remote Similarity NPD8086 Approved
0.6078 Remote Similarity NPD8138 Approved
0.6078 Remote Similarity NPD8139 Approved
0.6078 Remote Similarity NPD8083 Approved
0.6078 Remote Similarity NPD8084 Approved
0.6078 Remote Similarity NPD8085 Approved
0.6078 Remote Similarity NPD8082 Approved
0.6026 Remote Similarity NPD3198 Approved
0.6019 Remote Similarity NPD8276 Approved
0.6019 Remote Similarity NPD8275 Approved
0.5977 Remote Similarity NPD2257 Approved
0.5962 Remote Similarity NPD8081 Approved
0.5952 Remote Similarity NPD2694 Approved
0.5952 Remote Similarity NPD2697 Approved
0.5952 Remote Similarity NPD2695 Approved
0.5952 Remote Similarity NPD2696 Approved
0.5905 Remote Similarity NPD8393 Approved
0.5862 Remote Similarity NPD632 Discontinued
0.5857 Remote Similarity NPD2699 Approved
0.5849 Remote Similarity NPD8140 Approved
0.5849 Remote Similarity NPD8307 Discontinued
0.5833 Remote Similarity NPD4840 Approved
0.5833 Remote Similarity NPD4264 Clinical (unspecified phase)
0.5795 Remote Similarity NPD11 Approved
0.5795 Remote Similarity NPD376 Approved
0.5741 Remote Similarity NPD8306 Approved
0.5741 Remote Similarity NPD8305 Approved
0.5698 Remote Similarity NPD7535 Discontinued
0.5688 Remote Similarity NPD8087 Discontinued
0.5641 Remote Similarity NPD6439 Phase 3
0.561 Remote Similarity NPD1151 Approved
0.56 Remote Similarity NPD7348 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