Structure

Physi-Chem Properties

Molecular Weight:  549.38
Volume:  579.927
LogP:  2.481
LogD:  1.73
LogS:  -1.536
# Rotatable Bonds:  27
TPSA:  105.12
# H-Bond Aceptor:  8
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.047
Synthetic Accessibility Score:  3.919
Fsp3:  0.893
Lipinski Rule-of-5:  Accepted
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:  -5.358
MDCK Permeability:  3.658881178125739e-05
Pgp-inhibitor:  0.01
Pgp-substrate:  0.193
Human Intestinal Absorption (HIA):  0.908
20% Bioavailability (F20%):  0.982
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.003
Plasma Protein Binding (PPB):  94.8962173461914%
Volume Distribution (VD):  0.457
Pgp-substrate:  2.164848566055298%

ADMET: Metabolism

CYP1A2-inhibitor:  0.026
CYP1A2-substrate:  0.938
CYP2C19-inhibitor:  0.266
CYP2C19-substrate:  0.242
CYP2C9-inhibitor:  0.075
CYP2C9-substrate:  0.96
CYP2D6-inhibitor:  0.021
CYP2D6-substrate:  0.9
CYP3A4-inhibitor:  0.868
CYP3A4-substrate:  0.028

ADMET: Excretion

Clearance (CL):  3.525
Half-life (T1/2):  0.919

ADMET: Toxicity

hERG Blockers:  0.586
Human Hepatotoxicity (H-HT):  0.195
Drug-inuced Liver Injury (DILI):  0.006
AMES Toxicity:  0.103
Rat Oral Acute Toxicity:  0.125
Maximum Recommended Daily Dose:  0.933
Skin Sensitization:  0.936
Carcinogencity:  0.209
Eye Corrosion:  0.004
Eye Irritation:  0.012
Respiratory Toxicity:  0.671

Download Data

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

  Natural Product: NPC178758

Natural Product ID:  NPC178758
Common Name*:   1-O-(13'z-Eicosaenoyl)-Sn-Glycero-3-Phosphocholine
IUPAC Name:   [(2R)-2-hydroxy-3-[(Z)-icos-13-enoyl]oxypropyl] 2-(trimethylazaniumyl)ethyl phosphate
Synonyms:  
Standard InCHIKey:  JOPPVTHMSDTTEL-KDFWIBFYSA-N
Standard InCHI:  InChI=1S/C28H56NO7P/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-28(31)34-25-27(30)26-36-37(32,33)35-24-23-29(2,3)4/h10-11,27,30H,5-9,12-26H2,1-4H3/b11-10-/t27-/m1/s1
SMILES:  CCCCCC/C=CCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(OCC[N+](C)(C)C)[O-])O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL469489
PubChem CID:   10745243
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000256] Glycerophospholipids
        • [CHEMONTID:0002213] Glycerophosphocholines
          • [CHEMONTID:0001413] Lysophosphatidylcholines
            • [CHEMONTID:0001638] 1-acyl-sn-glycero-3-phosphocholines

*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
NPO85 Spirastrella abata Species Spirastrellidae Eukaryota n.a. n.a. n.a. PMID[10579872]
NPO85 Spirastrella abata Species Spirastrellidae Eukaryota n.a. n.a. n.a. PMID[11325244]
NPO85 Spirastrella abata Species Spirastrellidae Eukaryota n.a. n.a. n.a. PMID[12088447]
NPO85 Spirastrella abata Species Spirastrellidae Eukaryota n.a. n.a. n.a. PMID[22182501]

☑ 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
NPT2 Others Unspecified IC50 = 21.0 ug.mL-1 PMID[449799]

☑ 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 NPC178758 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 NPC196102
0.8974 High Similarity NPC325936
0.8701 High Similarity NPC305223
0.8442 Intermediate Similarity NPC114640
0.8442 Intermediate Similarity NPC126366
0.8442 Intermediate Similarity NPC170963
0.8442 Intermediate Similarity NPC169976
0.8442 Intermediate Similarity NPC33267
0.8442 Intermediate Similarity NPC324165
0.8312 Intermediate Similarity NPC475930
0.8312 Intermediate Similarity NPC127145
0.8205 Intermediate Similarity NPC474674
0.8077 Intermediate Similarity NPC137620
0.8077 Intermediate Similarity NPC474675
0.7821 Intermediate Similarity NPC104537
0.7821 Intermediate Similarity NPC127091
0.7821 Intermediate Similarity NPC330426
0.7821 Intermediate Similarity NPC148192
0.7821 Intermediate Similarity NPC473829
0.7821 Intermediate Similarity NPC271921
0.7821 Intermediate Similarity NPC475443
0.7821 Intermediate Similarity NPC22101
0.7802 Intermediate Similarity NPC329906
0.7722 Intermediate Similarity NPC473559
0.7722 Intermediate Similarity NPC141481
0.7722 Intermediate Similarity NPC324981
0.7722 Intermediate Similarity NPC320663
0.7722 Intermediate Similarity NPC224700
0.7722 Intermediate Similarity NPC48218
0.7654 Intermediate Similarity NPC54460
0.7647 Intermediate Similarity NPC474702
0.7625 Intermediate Similarity NPC473772
0.7531 Intermediate Similarity NPC476660
0.75 Intermediate Similarity NPC330017
0.7391 Intermediate Similarity NPC39290
0.7391 Intermediate Similarity NPC159369
0.7317 Intermediate Similarity NPC42526
0.7308 Intermediate Similarity NPC54925
0.7262 Intermediate Similarity NPC474321
0.7143 Intermediate Similarity NPC328786
0.7143 Intermediate Similarity NPC201338
0.7143 Intermediate Similarity NPC474627
0.7126 Intermediate Similarity NPC317263
0.7125 Intermediate Similarity NPC476654
0.7125 Intermediate Similarity NPC476657
0.7125 Intermediate Similarity NPC476655
0.7051 Intermediate Similarity NPC321919
0.7051 Intermediate Similarity NPC81896
0.7037 Intermediate Similarity NPC476659
0.7037 Intermediate Similarity NPC476656
0.6962 Remote Similarity NPC201939
0.6962 Remote Similarity NPC321838
0.6951 Remote Similarity NPC99619
0.6951 Remote Similarity NPC26500
0.6932 Remote Similarity NPC474833
0.6889 Remote Similarity NPC82799
0.6867 Remote Similarity NPC209327
0.6867 Remote Similarity NPC273508
0.6835 Remote Similarity NPC243532
0.679 Remote Similarity NPC68343
0.679 Remote Similarity NPC476658
0.679 Remote Similarity NPC328089
0.6742 Remote Similarity NPC218817
0.6742 Remote Similarity NPC11796
0.6707 Remote Similarity NPC176215
0.6707 Remote Similarity NPC296436
0.6707 Remote Similarity NPC238646
0.6705 Remote Similarity NPC49392
0.6705 Remote Similarity NPC190400
0.6703 Remote Similarity NPC21693
0.6703 Remote Similarity NPC236649
0.663 Remote Similarity NPC474312
0.6627 Remote Similarity NPC83965
0.6623 Remote Similarity NPC10316
0.6623 Remote Similarity NPC223677
0.6623 Remote Similarity NPC200845
0.6623 Remote Similarity NPC128061
0.6623 Remote Similarity NPC28779
0.6559 Remote Similarity NPC470313
0.6559 Remote Similarity NPC473500
0.6559 Remote Similarity NPC38295
0.6559 Remote Similarity NPC156089
0.6552 Remote Similarity NPC470435
0.6548 Remote Similarity NPC25298
0.6543 Remote Similarity NPC328776
0.6543 Remote Similarity NPC320305
0.6514 Remote Similarity NPC261750
0.6514 Remote Similarity NPC1111
0.6506 Remote Similarity NPC245947
0.6506 Remote Similarity NPC255863
0.6506 Remote Similarity NPC326268
0.6506 Remote Similarity NPC318420
0.6506 Remote Similarity NPC136164
0.6484 Remote Similarity NPC263574
0.6484 Remote Similarity NPC469747
0.6476 Remote Similarity NPC74035
0.6456 Remote Similarity NPC323436
0.642 Remote Similarity NPC229252
0.642 Remote Similarity NPC143857
0.6413 Remote Similarity NPC103634
0.6413 Remote Similarity NPC200446
0.6395 Remote Similarity NPC470436
0.6395 Remote Similarity NPC130618
0.6395 Remote Similarity NPC317583
0.6386 Remote Similarity NPC470320
0.6383 Remote Similarity NPC253801
0.6364 Remote Similarity NPC39633
0.6364 Remote Similarity NPC325627
0.6364 Remote Similarity NPC309606
0.6364 Remote Similarity NPC139545
0.6364 Remote Similarity NPC60432
0.6364 Remote Similarity NPC71761
0.6354 Remote Similarity NPC258824
0.6353 Remote Similarity NPC473357
0.6353 Remote Similarity NPC193029
0.6353 Remote Similarity NPC478100
0.6333 Remote Similarity NPC470899
0.6329 Remote Similarity NPC477201
0.6322 Remote Similarity NPC321873
0.6322 Remote Similarity NPC470268
0.6322 Remote Similarity NPC324638
0.6316 Remote Similarity NPC163093
0.631 Remote Similarity NPC325117
0.631 Remote Similarity NPC322319
0.631 Remote Similarity NPC326651
0.6304 Remote Similarity NPC209995
0.6282 Remote Similarity NPC469937
0.6282 Remote Similarity NPC87564
0.6282 Remote Similarity NPC261831
0.6282 Remote Similarity NPC6095
0.6282 Remote Similarity NPC23155
0.6282 Remote Similarity NPC53463
0.6282 Remote Similarity NPC290563
0.6282 Remote Similarity NPC424
0.6282 Remote Similarity NPC154245
0.6282 Remote Similarity NPC25417
0.6282 Remote Similarity NPC320588
0.6282 Remote Similarity NPC281972
0.6282 Remote Similarity NPC32467
0.6282 Remote Similarity NPC88966
0.6282 Remote Similarity NPC85813
0.6279 Remote Similarity NPC474812
0.6277 Remote Similarity NPC474252
0.6277 Remote Similarity NPC11332
0.6277 Remote Similarity NPC65930
0.6277 Remote Similarity NPC329829
0.6277 Remote Similarity NPC473712
0.6277 Remote Similarity NPC473780
0.6277 Remote Similarity NPC180363
0.6277 Remote Similarity NPC94875
0.6277 Remote Similarity NPC475159
0.6277 Remote Similarity NPC473529
0.6277 Remote Similarity NPC131002
0.6277 Remote Similarity NPC477487
0.6277 Remote Similarity NPC73310
0.6277 Remote Similarity NPC145914
0.6275 Remote Similarity NPC175614
0.6264 Remote Similarity NPC110813
0.625 Remote Similarity NPC120398
0.625 Remote Similarity NPC471567
0.625 Remote Similarity NPC475206
0.625 Remote Similarity NPC477014
0.625 Remote Similarity NPC477013
0.625 Remote Similarity NPC320119
0.625 Remote Similarity NPC322529
0.6235 Remote Similarity NPC478101
0.6222 Remote Similarity NPC3094
0.6211 Remote Similarity NPC144415
0.6207 Remote Similarity NPC143396
0.6203 Remote Similarity NPC228473
0.6203 Remote Similarity NPC52264
0.6196 Remote Similarity NPC133377
0.6196 Remote Similarity NPC469495
0.6195 Remote Similarity NPC30196
0.619 Remote Similarity NPC226592
0.6186 Remote Similarity NPC309211
0.6186 Remote Similarity NPC69082
0.6186 Remote Similarity NPC477015
0.6186 Remote Similarity NPC279267
0.618 Remote Similarity NPC326024
0.6163 Remote Similarity NPC478097
0.6154 Remote Similarity NPC294548
0.6154 Remote Similarity NPC36061
0.6154 Remote Similarity NPC1813
0.6154 Remote Similarity NPC70387
0.6154 Remote Similarity NPC321062
0.6154 Remote Similarity NPC139029
0.6146 Remote Similarity NPC9868
0.6146 Remote Similarity NPC156804
0.6145 Remote Similarity NPC66460
0.6145 Remote Similarity NPC271282
0.6145 Remote Similarity NPC325929
0.6145 Remote Similarity NPC113293
0.614 Remote Similarity NPC6531
0.6136 Remote Similarity NPC97614
0.6125 Remote Similarity NPC18951
0.6122 Remote Similarity NPC178215
0.6111 Remote Similarity NPC227396
0.6111 Remote Similarity NPC288086
0.6104 Remote Similarity NPC262968

  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 NPC178758 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
0.7848 Intermediate Similarity NPD8277 Approved
0.7722 Intermediate Similarity NPD8278 Approved
0.7403 Intermediate Similarity NPD6949 Clinical (unspecified phase)
0.7 Intermediate Similarity NPD3197 Phase 1
0.6818 Remote Similarity NPD7756 Clinical (unspecified phase)
0.6623 Remote Similarity NPD6950 Discontinued
0.6322 Remote Similarity NPD3212 Clinical (unspecified phase)
0.6283 Remote Similarity NPD6935 Phase 3
0.6283 Remote Similarity NPD6936 Clinical (unspecified phase)
0.6282 Remote Similarity NPD3194 Approved
0.6282 Remote Similarity NPD3196 Approved
0.6282 Remote Similarity NPD4266 Approved
0.6282 Remote Similarity NPD3730 Approved
0.6282 Remote Similarity NPD3728 Approved
0.6282 Remote Similarity NPD3195 Phase 2
0.6228 Remote Similarity NPD7641 Discontinued
0.6196 Remote Similarity NPD3732 Approved
0.6173 Remote Similarity NPD6109 Phase 1
0.6154 Remote Similarity NPD3172 Approved
0.6145 Remote Similarity NPD4283 Discontinued
0.6105 Remote Similarity NPD6435 Approved
0.6104 Remote Similarity NPD29 Approved
0.6104 Remote Similarity NPD28 Approved
0.6042 Remote Similarity NPD7154 Phase 3
0.604 Remote Similarity NPD7983 Approved
0.6036 Remote Similarity NPD6421 Discontinued
0.6024 Remote Similarity NPD4246 Clinical (unspecified phase)
0.598 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5948 Remote Similarity NPD6918 Phase 1
0.5941 Remote Similarity NPD46 Approved
0.5941 Remote Similarity NPD6698 Approved
0.5917 Remote Similarity NPD8341 Approved
0.5917 Remote Similarity NPD8342 Approved
0.5917 Remote Similarity NPD8340 Approved
0.5917 Remote Similarity NPD8299 Approved
0.5895 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5895 Remote Similarity NPD5368 Approved
0.5882 Remote Similarity NPD7347 Clinical (unspecified phase)
0.5868 Remote Similarity NPD8451 Approved
0.5833 Remote Similarity NPD7642 Approved
0.5833 Remote Similarity NPD5369 Approved
0.582 Remote Similarity NPD8448 Approved
0.581 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5795 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5784 Remote Similarity NPD8522 Clinical (unspecified phase)
0.5769 Remote Similarity NPD6948 Phase 3
0.5726 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6125 Clinical (unspecified phase)
0.5714 Remote Similarity NPD5362 Discontinued
0.5714 Remote Similarity NPD4840 Approved
0.5714 Remote Similarity NPD5343 Approved
0.5699 Remote Similarity NPD11 Approved
0.5699 Remote Similarity NPD376 Approved
0.5686 Remote Similarity NPD6101 Approved
0.5686 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5684 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5684 Remote Similarity NPD4268 Approved
0.5684 Remote Similarity NPD4271 Approved
0.568 Remote Similarity NPD8391 Approved
0.568 Remote Similarity NPD8390 Approved
0.568 Remote Similarity NPD8392 Approved
0.566 Remote Similarity NPD7839 Suspended
0.566 Remote Similarity NPD4228 Discovery
0.5641 Remote Similarity NPD3173 Approved
0.5638 Remote Similarity NPD818 Approved
0.5638 Remote Similarity NPD819 Approved
0.5615 Remote Similarity NPD8302 Clinical (unspecified phase)
0.5612 Remote Similarity NPD4269 Approved
0.5612 Remote Similarity NPD4270 Approved
0.561 Remote Similarity NPD8273 Phase 1

  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