Structure

Physi-Chem Properties

Molecular Weight:  308.31
Volume:  375.289
LogP:  7.992
LogD:  4.644
LogS:  -6.893
# Rotatable Bonds:  16
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.255
Synthetic Accessibility Score:  3.106
Fsp3:  0.905
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:  -4.752
MDCK Permeability:  1.1630349945335183e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.286
30% Bioavailability (F30%):  0.954

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.141
Plasma Protein Binding (PPB):  97.73771667480469%
Volume Distribution (VD):  2.286
Pgp-substrate:  0.9432830810546875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.36
CYP1A2-substrate:  0.181
CYP2C19-inhibitor:  0.608
CYP2C19-substrate:  0.101
CYP2C9-inhibitor:  0.378
CYP2C9-substrate:  0.976
CYP2D6-inhibitor:  0.289
CYP2D6-substrate:  0.042
CYP3A4-inhibitor:  0.284
CYP3A4-substrate:  0.068

ADMET: Excretion

Clearance (CL):  4.01
Half-life (T1/2):  0.056

ADMET: Toxicity

hERG Blockers:  0.034
Human Hepatotoxicity (H-HT):  0.141
Drug-inuced Liver Injury (DILI):  0.362
AMES Toxicity:  0.05
Rat Oral Acute Toxicity:  0.891
Maximum Recommended Daily Dose:  0.997
Skin Sensitization:  0.968
Carcinogencity:  0.105
Eye Corrosion:  0.98
Eye Irritation:  0.938
Respiratory Toxicity:  0.953

Download Data

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

  Natural Product: NPC473914

Natural Product ID:  NPC473914
Common Name*:   (3R)-16-Methylicos-1-Yn-3-Ol
IUPAC Name:   (3R)-16-methylicos-1-yn-3-ol
Synonyms:  
Standard InCHIKey:  HTNYAKWOWALLGI-LBAQZLPGSA-N
Standard InCHI:  InChI=1S/C21H40O/c1-4-6-17-20(3)18-15-13-11-9-7-8-10-12-14-16-19-21(22)5-2/h2,20-22H,4,6-19H2,1,3H3/t20?,21-/m0/s1
SMILES:  CCCCC(C)CCCCCCCCCCCCC(C#C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL455212
PubChem CID:   10403044
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
NPO15047 Cribrochalina vasculum Species Niphatidae Eukaryota n.a. Caribbean n.a. PMID[1431945]
NPO15047 Cribrochalina vasculum Species Niphatidae Eukaryota n.a. n.a. n.a. PMID[8691203]
NPO15047 Cribrochalina vasculum Species Niphatidae Eukaryota n.a. n.a. n.a. PMID[8984159]
NPO15047 Cribrochalina vasculum Species Niphatidae 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
NPT176 Organism Artemia salina Artemia salina LC50 = 1.2 ug.mL-1 PMID[565757]

☑ 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 NPC473914 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
0.9762 High Similarity NPC215358
0.8571 High Similarity NPC221022
0.814 Intermediate Similarity NPC471282
0.8095 Intermediate Similarity NPC177022
0.7955 Intermediate Similarity NPC160261
0.7955 Intermediate Similarity NPC469759
0.7619 Intermediate Similarity NPC97967
0.7447 Intermediate Similarity NPC144891
0.7442 Intermediate Similarity NPC474914
0.7442 Intermediate Similarity NPC474392
0.7381 Intermediate Similarity NPC283682
0.7347 Intermediate Similarity NPC198540
0.7347 Intermediate Similarity NPC84030
0.7347 Intermediate Similarity NPC176309
0.7347 Intermediate Similarity NPC147343
0.7347 Intermediate Similarity NPC223468
0.7347 Intermediate Similarity NPC287550
0.7143 Intermediate Similarity NPC319034
0.7143 Intermediate Similarity NPC181516
0.7143 Intermediate Similarity NPC205141
0.7143 Intermediate Similarity NPC193062
0.7143 Intermediate Similarity NPC185538
0.7143 Intermediate Similarity NPC272998
0.7143 Intermediate Similarity NPC66124
0.7143 Intermediate Similarity NPC72324
0.7143 Intermediate Similarity NPC139131
0.7143 Intermediate Similarity NPC291158
0.7143 Intermediate Similarity NPC1748
0.7045 Intermediate Similarity NPC328441
0.6939 Remote Similarity NPC62014
0.6905 Remote Similarity NPC122962
0.6905 Remote Similarity NPC267243
0.6905 Remote Similarity NPC126915
0.6863 Remote Similarity NPC314087
0.68 Remote Similarity NPC87439
0.6744 Remote Similarity NPC152759
0.6744 Remote Similarity NPC12231
0.6667 Remote Similarity NPC8597
0.6667 Remote Similarity NPC236797
0.6667 Remote Similarity NPC147096
0.6667 Remote Similarity NPC163556
0.6667 Remote Similarity NPC185041
0.6667 Remote Similarity NPC225783
0.6667 Remote Similarity NPC322148
0.6667 Remote Similarity NPC61665
0.6667 Remote Similarity NPC112242
0.6667 Remote Similarity NPC24506
0.66 Remote Similarity NPC240994
0.6545 Remote Similarity NPC475560
0.6545 Remote Similarity NPC161473
0.6531 Remote Similarity NPC474126
0.6531 Remote Similarity NPC474125
0.6522 Remote Similarity NPC74352
0.6491 Remote Similarity NPC474643
0.6491 Remote Similarity NPC473865
0.6481 Remote Similarity NPC307022
0.6441 Remote Similarity NPC122239
0.6429 Remote Similarity NPC53209
0.6429 Remote Similarity NPC289979
0.6429 Remote Similarity NPC110884
0.6415 Remote Similarity NPC304162
0.6406 Remote Similarity NPC82315
0.6379 Remote Similarity NPC135438
0.6364 Remote Similarity NPC295765
0.6316 Remote Similarity NPC277917
0.6316 Remote Similarity NPC166894
0.6316 Remote Similarity NPC178223
0.6316 Remote Similarity NPC89069
0.6316 Remote Similarity NPC283655
0.6316 Remote Similarity NPC84824
0.6316 Remote Similarity NPC471269
0.6316 Remote Similarity NPC474644
0.6316 Remote Similarity NPC67508
0.6296 Remote Similarity NPC131623
0.6275 Remote Similarity NPC469781
0.625 Remote Similarity NPC26102
0.625 Remote Similarity NPC187361
0.625 Remote Similarity NPC477724
0.623 Remote Similarity NPC148174
0.623 Remote Similarity NPC71460
0.623 Remote Similarity NPC218585
0.6226 Remote Similarity NPC324793
0.6226 Remote Similarity NPC477878
0.6222 Remote Similarity NPC139569
0.6207 Remote Similarity NPC24443
0.619 Remote Similarity NPC52362
0.619 Remote Similarity NPC223195
0.619 Remote Similarity NPC279895
0.619 Remote Similarity NPC159845
0.6167 Remote Similarity NPC470363
0.6154 Remote Similarity NPC77550
0.6154 Remote Similarity NPC108441
0.6129 Remote Similarity NPC279200
0.6129 Remote Similarity NPC114891
0.6129 Remote Similarity NPC290791
0.6129 Remote Similarity NPC292419
0.6102 Remote Similarity NPC150713
0.6102 Remote Similarity NPC29976
0.6102 Remote Similarity NPC236588
0.6102 Remote Similarity NPC291147
0.6102 Remote Similarity NPC119425
0.6061 Remote Similarity NPC28526
0.6042 Remote Similarity NPC469712
0.6042 Remote Similarity NPC469714
0.6042 Remote Similarity NPC473568
0.6042 Remote Similarity NPC197039
0.6038 Remote Similarity NPC324004
0.6038 Remote Similarity NPC14552
0.6038 Remote Similarity NPC21844
0.6038 Remote Similarity NPC328497
0.6034 Remote Similarity NPC477725
0.6034 Remote Similarity NPC477726
0.6032 Remote Similarity NPC118937
0.6032 Remote Similarity NPC225415
0.6032 Remote Similarity NPC281540
0.6032 Remote Similarity NPC167995
0.6032 Remote Similarity NPC476702
0.6032 Remote Similarity NPC69149
0.6032 Remote Similarity NPC159654
0.6032 Remote Similarity NPC290367
0.6032 Remote Similarity NPC309300
0.6 Remote Similarity NPC226848
0.6 Remote Similarity NPC47663
0.6 Remote Similarity NPC475830
0.6 Remote Similarity NPC215671
0.6 Remote Similarity NPC476735
0.6 Remote Similarity NPC475515
0.6 Remote Similarity NPC474361
0.6 Remote Similarity NPC87296
0.5968 Remote Similarity NPC274704
0.5968 Remote Similarity NPC475251
0.5962 Remote Similarity NPC313795
0.5952 Remote Similarity NPC39869
0.5952 Remote Similarity NPC276332
0.5938 Remote Similarity NPC473276
0.5938 Remote Similarity NPC238352
0.5938 Remote Similarity NPC260116
0.5938 Remote Similarity NPC472946
0.5938 Remote Similarity NPC80463
0.5938 Remote Similarity NPC41577
0.5938 Remote Similarity NPC308844
0.5938 Remote Similarity NPC477009
0.5938 Remote Similarity NPC474380
0.5938 Remote Similarity NPC476330
0.5932 Remote Similarity NPC470968
0.5932 Remote Similarity NPC470966
0.5932 Remote Similarity NPC471960
0.5932 Remote Similarity NPC475384
0.5932 Remote Similarity NPC161838
0.5932 Remote Similarity NPC470969
0.5932 Remote Similarity NPC477661
0.5932 Remote Similarity NPC470967
0.5932 Remote Similarity NPC473847
0.5926 Remote Similarity NPC106872
0.5902 Remote Similarity NPC475968
0.5902 Remote Similarity NPC185116
0.5902 Remote Similarity NPC475931
0.5893 Remote Similarity NPC100096
0.5873 Remote Similarity NPC474552
0.5862 Remote Similarity NPC286752
0.5862 Remote Similarity NPC49059
0.5862 Remote Similarity NPC256209
0.5849 Remote Similarity NPC314679
0.5846 Remote Similarity NPC142712
0.5846 Remote Similarity NPC272125
0.5846 Remote Similarity NPC44122
0.5833 Remote Similarity NPC470970
0.5833 Remote Similarity NPC52012
0.5818 Remote Similarity NPC294858
0.5818 Remote Similarity NPC95969
0.5818 Remote Similarity NPC127997
0.5818 Remote Similarity NPC316035
0.5806 Remote Similarity NPC475412
0.58 Remote Similarity NPC152008
0.5781 Remote Similarity NPC314103
0.5763 Remote Similarity NPC281590
0.5763 Remote Similarity NPC473896
0.5763 Remote Similarity NPC473721
0.5763 Remote Similarity NPC223604
0.5763 Remote Similarity NPC475353
0.5763 Remote Similarity NPC473735
0.5763 Remote Similarity NPC473725
0.5763 Remote Similarity NPC473910
0.5758 Remote Similarity NPC475884
0.5758 Remote Similarity NPC114651
0.5758 Remote Similarity NPC477758
0.5758 Remote Similarity NPC48079
0.5758 Remote Similarity NPC473230
0.5758 Remote Similarity NPC477761
0.5758 Remote Similarity NPC259299
0.5758 Remote Similarity NPC472984
0.5758 Remote Similarity NPC472253
0.5758 Remote Similarity NPC477759
0.5758 Remote Similarity NPC204233
0.5758 Remote Similarity NPC472255
0.5758 Remote Similarity NPC477760
0.5758 Remote Similarity NPC477754
0.5714 Remote Similarity NPC95804
0.5714 Remote Similarity NPC172622
0.5714 Remote Similarity NPC185547

  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 NPC473914 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
0.7347 Intermediate Similarity NPD385 Approved
0.7347 Intermediate Similarity NPD384 Approved
0.7143 Intermediate Similarity NPD5383 Approved
0.7143 Intermediate Similarity NPD2272 Approved
0.6875 Remote Similarity NPD1462 Approved
0.6809 Remote Similarity NPD1460 Approved
0.6462 Remote Similarity NPD4787 Phase 1
0.6441 Remote Similarity NPD3198 Approved
0.6429 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6154 Remote Similarity NPD386 Approved
0.6154 Remote Similarity NPD388 Approved
0.6032 Remote Similarity NPD7909 Approved
0.5849 Remote Similarity NPD634 Phase 3
0.58 Remote Similarity NPD7536 Approved
0.5789 Remote Similarity NPD3186 Phase 1
0.5714 Remote Similarity NPD3214 Discontinued
0.5614 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