Structure

Physi-Chem Properties

Molecular Weight:  300.27
Volume:  343.618
LogP:  5.922
LogD:  3.677
LogS:  -5.733
# Rotatable Bonds:  17
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.322
Synthetic Accessibility Score:  1.891
Fsp3:  0.944
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.807
MDCK Permeability:  2.191248131566681e-05
Pgp-inhibitor:  0.025
Pgp-substrate:  0.01
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.927
30% Bioavailability (F30%):  0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.295
Plasma Protein Binding (PPB):  96.27349090576172%
Volume Distribution (VD):  1.109
Pgp-substrate:  1.6774770021438599%

ADMET: Metabolism

CYP1A2-inhibitor:  0.559
CYP1A2-substrate:  0.195
CYP2C19-inhibitor:  0.364
CYP2C19-substrate:  0.057
CYP2C9-inhibitor:  0.238
CYP2C9-substrate:  0.937
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.05
CYP3A4-inhibitor:  0.319
CYP3A4-substrate:  0.05

ADMET: Excretion

Clearance (CL):  6.15
Half-life (T1/2):  0.44

ADMET: Toxicity

hERG Blockers:  0.176
Human Hepatotoxicity (H-HT):  0.034
Drug-inuced Liver Injury (DILI):  0.092
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.017
Maximum Recommended Daily Dose:  0.015
Skin Sensitization:  0.957
Carcinogencity:  0.07
Eye Corrosion:  0.92
Eye Irritation:  0.955
Respiratory Toxicity:  0.746

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

  Natural Product: NPC12438

Natural Product ID:  NPC12438
Common Name*:   Methyl 17-Hydroxyheptadecanoate
IUPAC Name:   methyl 17-hydroxyheptadecanoate
Synonyms:   Methyl Omega-Hydroxyheptadecanoate
Standard InCHIKey:  UVIQCJHXPJPAOJ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C18H36O3/c1-21-18(20)16-14-12-10-8-6-4-2-3-5-7-9-11-13-15-17-19/h19H,2-17H2,1H3
SMILES:  OCCCCCCCCCCCCCCCCC(=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL477885
PubChem CID:   13245691
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols
          • [CHEMONTID:0002951] Long-chain fatty alcohols

*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
NPT81 Cell Line A549 Homo sapiens ED50 > 30.0 ug ml-1 PMID[512854]
NPT146 Cell Line SK-OV-3 Homo sapiens ED50 > 30.0 ug ml-1 PMID[512854]
NPT147 Cell Line SK-MEL-2 Homo sapiens ED50 > 30.0 ug ml-1 PMID[512854]
NPT574 Cell Line XF498 Homo sapiens ED50 > 30.0 ug ml-1 PMID[512854]
NPT148 Cell Line HCT-15 Homo sapiens ED50 > 30.0 ug ml-1 PMID[512854]

☑ 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 NPC12438 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 NPC30195
0.9545 High Similarity NPC106872
0.9318 High Similarity NPC324004
0.9318 High Similarity NPC328497
0.9048 High Similarity NPC171736
0.9048 High Similarity NPC196924
0.9048 High Similarity NPC307783
0.9048 High Similarity NPC209970
0.9048 High Similarity NPC216630
0.9048 High Similarity NPC149184
0.8913 High Similarity NPC26253
0.8837 High Similarity NPC236579
0.8837 High Similarity NPC203531
0.8837 High Similarity NPC67462
0.881 High Similarity NPC28598
0.881 High Similarity NPC161097
0.8723 High Similarity NPC90904
0.8636 High Similarity NPC74845
0.8571 High Similarity NPC301585
0.8571 High Similarity NPC113928
0.8571 High Similarity NPC261080
0.8571 High Similarity NPC154186
0.8571 High Similarity NPC301696
0.8571 High Similarity NPC14227
0.8571 High Similarity NPC279026
0.8571 High Similarity NPC201844
0.8511 High Similarity NPC304162
0.8444 Intermediate Similarity NPC47363
0.8444 Intermediate Similarity NPC469781
0.8444 Intermediate Similarity NPC8219
0.8444 Intermediate Similarity NPC287231
0.84 Intermediate Similarity NPC23155
0.84 Intermediate Similarity NPC469937
0.84 Intermediate Similarity NPC53463
0.84 Intermediate Similarity NPC320588
0.8372 Intermediate Similarity NPC250028
0.8372 Intermediate Similarity NPC165533
0.8372 Intermediate Similarity NPC12156
0.8372 Intermediate Similarity NPC256163
0.8372 Intermediate Similarity NPC40597
0.8372 Intermediate Similarity NPC149299
0.8333 Intermediate Similarity NPC54980
0.8333 Intermediate Similarity NPC305660
0.8333 Intermediate Similarity NPC201622
0.8333 Intermediate Similarity NPC22903
0.8298 Intermediate Similarity NPC200618
0.8298 Intermediate Similarity NPC131770
0.8222 Intermediate Similarity NPC255837
0.8222 Intermediate Similarity NPC19305
0.8182 Intermediate Similarity NPC53541
0.814 Intermediate Similarity NPC118968
0.814 Intermediate Similarity NPC214610
0.814 Intermediate Similarity NPC31551
0.814 Intermediate Similarity NPC223249
0.814 Intermediate Similarity NPC183424
0.814 Intermediate Similarity NPC294085
0.814 Intermediate Similarity NPC80234
0.814 Intermediate Similarity NPC219536
0.8085 Intermediate Similarity NPC21844
0.8 Intermediate Similarity NPC71317
0.8 Intermediate Similarity NPC301528
0.8 Intermediate Similarity NPC129972
0.7917 Intermediate Similarity NPC477878
0.7917 Intermediate Similarity NPC324793
0.7907 Intermediate Similarity NPC268826
0.7857 Intermediate Similarity NPC155263
0.7826 Intermediate Similarity NPC76051
0.7826 Intermediate Similarity NPC317128
0.78 Intermediate Similarity NPC100096
0.7778 Intermediate Similarity NPC163746
0.7778 Intermediate Similarity NPC103286
0.7674 Intermediate Similarity NPC128996
0.766 Intermediate Similarity NPC55023
0.7636 Intermediate Similarity NPC470363
0.7619 Intermediate Similarity NPC156630
0.7619 Intermediate Similarity NPC317203
0.76 Intermediate Similarity NPC55678
0.75 Intermediate Similarity NPC52700
0.75 Intermediate Similarity NPC145045
0.75 Intermediate Similarity NPC63182
0.75 Intermediate Similarity NPC105329
0.75 Intermediate Similarity NPC314679
0.7451 Intermediate Similarity NPC287811
0.7442 Intermediate Similarity NPC80641
0.7442 Intermediate Similarity NPC134782
0.7442 Intermediate Similarity NPC154642
0.7442 Intermediate Similarity NPC80396
0.7368 Intermediate Similarity NPC201939
0.7347 Intermediate Similarity NPC249754
0.7347 Intermediate Similarity NPC326957
0.7308 Intermediate Similarity NPC310746
0.7292 Intermediate Similarity NPC273545
0.7273 Intermediate Similarity NPC74352
0.7241 Intermediate Similarity NPC235788
0.7209 Intermediate Similarity NPC301398
0.7209 Intermediate Similarity NPC86545
0.7209 Intermediate Similarity NPC196442
0.7209 Intermediate Similarity NPC223374
0.7193 Intermediate Similarity NPC243532
0.717 Intermediate Similarity NPC72722
0.7143 Intermediate Similarity NPC308301
0.7143 Intermediate Similarity NPC185538
0.7143 Intermediate Similarity NPC272998
0.7143 Intermediate Similarity NPC139131
0.7143 Intermediate Similarity NPC175342
0.7143 Intermediate Similarity NPC152759
0.7143 Intermediate Similarity NPC181516
0.7143 Intermediate Similarity NPC12231
0.7143 Intermediate Similarity NPC205141
0.7143 Intermediate Similarity NPC291158
0.7119 Intermediate Similarity NPC314103
0.7115 Intermediate Similarity NPC470410
0.7115 Intermediate Similarity NPC470412
0.7111 Intermediate Similarity NPC73245
0.7045 Intermediate Similarity NPC474392
0.7045 Intermediate Similarity NPC474914
0.7037 Intermediate Similarity NPC25417
0.7037 Intermediate Similarity NPC87564
0.7037 Intermediate Similarity NPC281972
0.7037 Intermediate Similarity NPC261831
0.7037 Intermediate Similarity NPC32467
0.7037 Intermediate Similarity NPC154245
0.7037 Intermediate Similarity NPC6095
0.7037 Intermediate Similarity NPC88966
0.7037 Intermediate Similarity NPC424
0.7037 Intermediate Similarity NPC85813
0.7037 Intermediate Similarity NPC87394
0.7037 Intermediate Similarity NPC290563
0.7021 Intermediate Similarity NPC325452
0.7021 Intermediate Similarity NPC248763
0.7018 Intermediate Similarity NPC17935
0.7 Intermediate Similarity NPC476330
0.6977 Remote Similarity NPC154396
0.6977 Remote Similarity NPC286498
0.6977 Remote Similarity NPC57499
0.6957 Remote Similarity NPC81263
0.6923 Remote Similarity NPC305182
0.6909 Remote Similarity NPC128061
0.6909 Remote Similarity NPC200845
0.6909 Remote Similarity NPC10316
0.6909 Remote Similarity NPC28779
0.6909 Remote Similarity NPC223677
0.6905 Remote Similarity NPC126915
0.6889 Remote Similarity NPC158179
0.6875 Remote Similarity NPC289686
0.6875 Remote Similarity NPC176500
0.6863 Remote Similarity NPC216130
0.6863 Remote Similarity NPC180534
0.6852 Remote Similarity NPC321062
0.6852 Remote Similarity NPC294548
0.6852 Remote Similarity NPC139029
0.6852 Remote Similarity NPC309606
0.6852 Remote Similarity NPC1813
0.6852 Remote Similarity NPC36061
0.6852 Remote Similarity NPC39633
0.6852 Remote Similarity NPC70387
0.6852 Remote Similarity NPC139545
0.6833 Remote Similarity NPC68343
0.6833 Remote Similarity NPC328089
0.6818 Remote Similarity NPC97967
0.68 Remote Similarity NPC166287
0.6792 Remote Similarity NPC314084
0.6786 Remote Similarity NPC477201
0.6786 Remote Similarity NPC18951
0.678 Remote Similarity NPC469923
0.6774 Remote Similarity NPC127091
0.6774 Remote Similarity NPC206601
0.6774 Remote Similarity NPC271921
0.6774 Remote Similarity NPC330426
0.6774 Remote Similarity NPC22101
0.6774 Remote Similarity NPC469925
0.6774 Remote Similarity NPC104537
0.6774 Remote Similarity NPC148192
0.6774 Remote Similarity NPC286842
0.6744 Remote Similarity NPC286695
0.6744 Remote Similarity NPC328710
0.6744 Remote Similarity NPC322892
0.6744 Remote Similarity NPC18224
0.6739 Remote Similarity NPC197039
0.6731 Remote Similarity NPC250919
0.6727 Remote Similarity NPC289979
0.6724 Remote Similarity NPC469924
0.6721 Remote Similarity NPC245947
0.6721 Remote Similarity NPC255863
0.6721 Remote Similarity NPC136164
0.6667 Remote Similarity NPC163556
0.6667 Remote Similarity NPC225783
0.6667 Remote Similarity NPC281245
0.6667 Remote Similarity NPC236797
0.6667 Remote Similarity NPC185041
0.6667 Remote Similarity NPC324981
0.6667 Remote Similarity NPC161366
0.6667 Remote Similarity NPC24506
0.6667 Remote Similarity NPC147096
0.6667 Remote Similarity NPC473559
0.6667 Remote Similarity NPC48218
0.6667 Remote Similarity NPC474552
0.6667 Remote Similarity NPC141481
0.6667 Remote Similarity NPC92114
0.6667 Remote Similarity NPC112242

  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 NPC12438 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
0.9048 High Similarity NPD2270 Approved
0.8571 High Similarity NPD633 Phase 3
0.8571 High Similarity NPD9448 Phase 2
0.8444 Intermediate Similarity NPD2699 Approved
0.8444 Intermediate Similarity NPD3199 Clinical (unspecified phase)
0.84 Intermediate Similarity NPD3730 Approved
0.84 Intermediate Similarity NPD3728 Approved
0.8333 Intermediate Similarity NPD3206 Approved
0.814 Intermediate Similarity NPD9655 Approved
0.8039 Intermediate Similarity NPD3729 Clinical (unspecified phase)
0.7551 Intermediate Similarity NPD6125 Clinical (unspecified phase)
0.75 Intermediate Similarity NPD634 Phase 3
0.7321 Intermediate Similarity NPD3198 Approved
0.7308 Intermediate Similarity NPD3186 Phase 1
0.72 Intermediate Similarity NPD2266 Phase 2
0.7143 Intermediate Similarity NPD2272 Approved
0.7143 Intermediate Similarity NPD5383 Approved
0.7037 Intermediate Similarity NPD3196 Approved
0.7037 Intermediate Similarity NPD3195 Phase 2
0.7037 Intermediate Similarity NPD3194 Approved
0.7037 Intermediate Similarity NPD4266 Approved
0.6875 Remote Similarity NPD387 Clinical (unspecified phase)
0.6863 Remote Similarity NPD622 Approved
0.6852 Remote Similarity NPD3172 Approved
0.6833 Remote Similarity NPD7909 Approved
0.6833 Remote Similarity NPD3197 Phase 1
0.68 Remote Similarity NPD9430 Approved
0.68 Remote Similarity NPD9431 Approved
0.6596 Remote Similarity NPD77 Approved
0.6596 Remote Similarity NPD9450 Approved
0.6481 Remote Similarity NPD28 Approved
0.6481 Remote Similarity NPD29 Approved
0.6458 Remote Similarity NPD7536 Approved
0.6429 Remote Similarity NPD615 Clinical (unspecified phase)
0.6383 Remote Similarity NPD9513 Phase 1
0.6182 Remote Similarity NPD9638 Phase 2
0.617 Remote Similarity NPD9449 Clinical (unspecified phase)
0.6111 Remote Similarity NPD3173 Approved
0.6066 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5942 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5932 Remote Similarity NPD73 Approved
0.5909 Remote Similarity NPD8618 Approved
0.5882 Remote Similarity NPD2256 Clinical (unspecified phase)
0.587 Remote Similarity NPD8857 Approved
0.5846 Remote Similarity NPD3704 Approved
0.5821 Remote Similarity NPD8277 Approved
0.58 Remote Similarity NPD9635 Discontinued
0.5775 Remote Similarity NPD6117 Approved
0.5745 Remote Similarity NPD9447 Approved
0.5741 Remote Similarity NPD3211 Approved
0.5714 Remote Similarity NPD4283 Discontinued
0.5714 Remote Similarity NPD9676 Phase 3
0.5694 Remote Similarity NPD6116 Phase 1
0.5692 Remote Similarity NPD3171 Clinical (unspecified phase)
0.5682 Remote Similarity NPD8619 Approved
0.5682 Remote Similarity NPD8617 Approved
0.5672 Remote Similarity NPD8278 Approved
0.5636 Remote Similarity NPD5343 Approved
0.5634 Remote Similarity NPD2257 Approved
0.5634 Remote Similarity NPD3702 Approved
0.5616 Remote Similarity NPD4802 Phase 2
0.5616 Remote Similarity NPD6697 Approved
0.5616 Remote Similarity NPD6114 Approved
0.5616 Remote Similarity NPD3732 Approved
0.5616 Remote Similarity NPD6115 Approved
0.5616 Remote Similarity NPD4238 Approved
0.5616 Remote Similarity NPD6118 Approved
0.5606 Remote Similarity NPD4224 Phase 2
0.56 Remote Similarity NPD5369 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