Structure

Physi-Chem Properties

Molecular Weight:  344.24
Volume:  396.984
LogP:  4.897
LogD:  3.71
LogS:  -4.745
# Rotatable Bonds:  15
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.217
Synthetic Accessibility Score:  3.932
Fsp3:  0.591
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:  -4.868
MDCK Permeability:  1.8621503841131926e-05
Pgp-inhibitor:  0.015
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.955
20% Bioavailability (F20%):  0.992
30% Bioavailability (F30%):  0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.036
Plasma Protein Binding (PPB):  90.42302703857422%
Volume Distribution (VD):  0.906
Pgp-substrate:  1.1926625967025757%

ADMET: Metabolism

CYP1A2-inhibitor:  0.817
CYP1A2-substrate:  0.194
CYP2C19-inhibitor:  0.933
CYP2C19-substrate:  0.422
CYP2C9-inhibitor:  0.814
CYP2C9-substrate:  0.987
CYP2D6-inhibitor:  0.65
CYP2D6-substrate:  0.088
CYP3A4-inhibitor:  0.834
CYP3A4-substrate:  0.158

ADMET: Excretion

Clearance (CL):  2.464
Half-life (T1/2):  0.224

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.98
Drug-inuced Liver Injury (DILI):  0.57
AMES Toxicity:  0.885
Rat Oral Acute Toxicity:  0.955
Maximum Recommended Daily Dose:  0.999
Skin Sensitization:  0.955
Carcinogencity:  0.05
Eye Corrosion:  0.911
Eye Irritation:  0.939
Respiratory Toxicity:  0.986

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

  Natural Product: NPC471278

Natural Product ID:  NPC471278
Common Name*:   (3S,4E,16E,18R)-18-Hydroxyicosa-4,16-Dien-1,19-Diyn-3-Yl Acetate
IUPAC Name:   [(3S,4E,16E,18R)-18-hydroxyicosa-4,16-dien-1,19-diyn-3-yl] acetate
Synonyms:  
Standard InCHIKey:  HEFOAGVZRBHVPE-WABXBRDYSA-N
Standard InCHI:  InChI=1S/C22H32O3/c1-4-21(24)18-16-14-12-10-8-6-7-9-11-13-15-17-19-22(5-2)25-20(3)23/h1-2,16-19,21-22,24H,6-15H2,3H3/b18-16+,19-17+/t21-,22+/m0/s1
SMILES:  C#C[C@@H](OC(=O)C)/C=C/CCCCCCCCCC/C=C/[C@H](C#C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2408393
PubChem CID:   71747207
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
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. red sea n.a. PMID[12762806]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[18027906]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[22469701]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. collected by hand at a depth of 10 m off the shore of Iriomote Island, Okinawa Prefecture, Japan 2009-JUN PMID[23855338]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[24948562]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[27015002]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. New Guinea n.a. PMID[8158156]

☑ 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
NPT165 Cell Line HeLa Homo sapiens IC50 = 2700.0 nM PMID[491197]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 280.0 nM PMID[491197]

☑ 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 NPC471278 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
0.9464 High Similarity NPC265551
0.9464 High Similarity NPC212730
0.9123 High Similarity NPC471277
0.9123 High Similarity NPC471279
0.9107 High Similarity NPC146551
0.9107 High Similarity NPC470963
0.9107 High Similarity NPC474513
0.8947 High Similarity NPC311648
0.8947 High Similarity NPC470964
0.8793 High Similarity NPC48968
0.8793 High Similarity NPC594
0.8772 High Similarity NPC152668
0.8525 High Similarity NPC271282
0.8525 High Similarity NPC325929
0.8525 High Similarity NPC66460
0.85 High Similarity NPC222852
0.8475 Intermediate Similarity NPC44542
0.8387 Intermediate Similarity NPC29697
0.8276 Intermediate Similarity NPC48058
0.8276 Intermediate Similarity NPC269615
0.8226 Intermediate Similarity NPC475984
0.8214 Intermediate Similarity NPC474642
0.8214 Intermediate Similarity NPC199286
0.8214 Intermediate Similarity NPC471281
0.8214 Intermediate Similarity NPC477727
0.8214 Intermediate Similarity NPC473913
0.8214 Intermediate Similarity NPC249670
0.8197 Intermediate Similarity NPC474267
0.8167 Intermediate Similarity NPC472445
0.8095 Intermediate Similarity NPC470965
0.807 Intermediate Similarity NPC329608
0.807 Intermediate Similarity NPC475477
0.807 Intermediate Similarity NPC165447
0.807 Intermediate Similarity NPC89824
0.807 Intermediate Similarity NPC170776
0.807 Intermediate Similarity NPC294278
0.807 Intermediate Similarity NPC477723
0.807 Intermediate Similarity NPC76198
0.807 Intermediate Similarity NPC197272
0.807 Intermediate Similarity NPC224148
0.807 Intermediate Similarity NPC471959
0.807 Intermediate Similarity NPC9273
0.807 Intermediate Similarity NPC55383
0.807 Intermediate Similarity NPC256656
0.8036 Intermediate Similarity NPC248884
0.8036 Intermediate Similarity NPC125122
0.8036 Intermediate Similarity NPC471275
0.8036 Intermediate Similarity NPC31194
0.8036 Intermediate Similarity NPC471276
0.8036 Intermediate Similarity NPC85079
0.8036 Intermediate Similarity NPC471280
0.7931 Intermediate Similarity NPC142092
0.7931 Intermediate Similarity NPC106531
0.7895 Intermediate Similarity NPC72699
0.7869 Intermediate Similarity NPC193975
0.7833 Intermediate Similarity NPC471239
0.7833 Intermediate Similarity NPC474913
0.7778 Intermediate Similarity NPC299730
0.7759 Intermediate Similarity NPC151782
0.7719 Intermediate Similarity NPC153538
0.7679 Intermediate Similarity NPC124183
0.7679 Intermediate Similarity NPC55063
0.7679 Intermediate Similarity NPC35141
0.7679 Intermediate Similarity NPC19834
0.7667 Intermediate Similarity NPC473532
0.7656 Intermediate Similarity NPC26810
0.7619 Intermediate Similarity NPC473652
0.7612 Intermediate Similarity NPC225272
0.7581 Intermediate Similarity NPC129150
0.7541 Intermediate Similarity NPC473910
0.7541 Intermediate Similarity NPC477726
0.7541 Intermediate Similarity NPC473735
0.7541 Intermediate Similarity NPC473721
0.7541 Intermediate Similarity NPC473896
0.7541 Intermediate Similarity NPC475353
0.7541 Intermediate Similarity NPC473725
0.7541 Intermediate Similarity NPC474644
0.7541 Intermediate Similarity NPC477725
0.75 Intermediate Similarity NPC269074
0.7463 Intermediate Similarity NPC146811
0.746 Intermediate Similarity NPC469373
0.746 Intermediate Similarity NPC223679
0.7458 Intermediate Similarity NPC93639
0.7424 Intermediate Similarity NPC470320
0.7424 Intermediate Similarity NPC226592
0.7419 Intermediate Similarity NPC473865
0.7419 Intermediate Similarity NPC161838
0.7419 Intermediate Similarity NPC474643
0.7419 Intermediate Similarity NPC473847
0.7419 Intermediate Similarity NPC470968
0.7419 Intermediate Similarity NPC470966
0.7419 Intermediate Similarity NPC470967
0.7419 Intermediate Similarity NPC475384
0.7419 Intermediate Similarity NPC471960
0.7419 Intermediate Similarity NPC470969
0.7419 Intermediate Similarity NPC477661
0.7385 Intermediate Similarity NPC55376
0.7385 Intermediate Similarity NPC168407
0.7377 Intermediate Similarity NPC256209
0.7377 Intermediate Similarity NPC49059
0.7353 Intermediate Similarity NPC478097
0.7353 Intermediate Similarity NPC473752
0.7324 Intermediate Similarity NPC329890
0.7321 Intermediate Similarity NPC101616
0.7302 Intermediate Similarity NPC470970
0.7302 Intermediate Similarity NPC294938
0.7286 Intermediate Similarity NPC476037
0.7286 Intermediate Similarity NPC4299
0.7231 Intermediate Similarity NPC327112
0.7213 Intermediate Similarity NPC61177
0.7188 Intermediate Similarity NPC254095
0.7183 Intermediate Similarity NPC472254
0.7167 Intermediate Similarity NPC71053
0.7167 Intermediate Similarity NPC59408
0.7143 Intermediate Similarity NPC470436
0.7143 Intermediate Similarity NPC96663
0.7143 Intermediate Similarity NPC101622
0.7123 Intermediate Similarity NPC260396
0.7121 Intermediate Similarity NPC113293
0.7121 Intermediate Similarity NPC477829
0.7101 Intermediate Similarity NPC478100
0.7097 Intermediate Similarity NPC110732
0.7083 Intermediate Similarity NPC327383
0.7083 Intermediate Similarity NPC329914
0.7083 Intermediate Similarity NPC477085
0.7083 Intermediate Similarity NPC185186
0.7077 Intermediate Similarity NPC82465
0.7077 Intermediate Similarity NPC329424
0.7077 Intermediate Similarity NPC22897
0.7077 Intermediate Similarity NPC159650
0.7077 Intermediate Similarity NPC97570
0.7069 Intermediate Similarity NPC180575
0.7069 Intermediate Similarity NPC197467
0.7059 Intermediate Similarity NPC96414
0.7059 Intermediate Similarity NPC255863
0.7059 Intermediate Similarity NPC282760
0.7059 Intermediate Similarity NPC19769
0.7059 Intermediate Similarity NPC478098
0.7059 Intermediate Similarity NPC478099
0.7059 Intermediate Similarity NPC136164
0.7059 Intermediate Similarity NPC245947
0.7042 Intermediate Similarity NPC473361
0.7042 Intermediate Similarity NPC329904
0.7042 Intermediate Similarity NPC476012
0.7031 Intermediate Similarity NPC135863
0.7031 Intermediate Similarity NPC249850
0.7031 Intermediate Similarity NPC293437
0.7027 Intermediate Similarity NPC188860
0.7015 Intermediate Similarity NPC44343
0.7015 Intermediate Similarity NPC179087
0.7015 Intermediate Similarity NPC210303
0.7013 Intermediate Similarity NPC150502
0.7 Intermediate Similarity NPC291437
0.7 Intermediate Similarity NPC474823
0.7 Intermediate Similarity NPC328784
0.6964 Remote Similarity NPC57923
0.6964 Remote Similarity NPC149668
0.6964 Remote Similarity NPC304151
0.6957 Remote Similarity NPC201356
0.6957 Remote Similarity NPC478101
0.6944 Remote Similarity NPC186531
0.6944 Remote Similarity NPC477086
0.6944 Remote Similarity NPC316185
0.6944 Remote Similarity NPC293114
0.6944 Remote Similarity NPC477087
0.6935 Remote Similarity NPC477724
0.6935 Remote Similarity NPC477780
0.6935 Remote Similarity NPC187361
0.6935 Remote Similarity NPC26102
0.6935 Remote Similarity NPC477781
0.6933 Remote Similarity NPC233071
0.6923 Remote Similarity NPC21946
0.6923 Remote Similarity NPC474084
0.6912 Remote Similarity NPC476658
0.6901 Remote Similarity NPC151481
0.6901 Remote Similarity NPC475004
0.6897 Remote Similarity NPC47946
0.6897 Remote Similarity NPC26600
0.6892 Remote Similarity NPC327041
0.6892 Remote Similarity NPC285840
0.6885 Remote Similarity NPC474495
0.6885 Remote Similarity NPC473672
0.6885 Remote Similarity NPC129263
0.6875 Remote Similarity NPC472808
0.6875 Remote Similarity NPC324224
0.6866 Remote Similarity NPC201939
0.6866 Remote Similarity NPC320305
0.6866 Remote Similarity NPC328776
0.6857 Remote Similarity NPC122627
0.6857 Remote Similarity NPC99619
0.6857 Remote Similarity NPC26500
0.6849 Remote Similarity NPC470435
0.6849 Remote Similarity NPC284006
0.6842 Remote Similarity NPC473471
0.6842 Remote Similarity NPC248775
0.6833 Remote Similarity NPC207815
0.6833 Remote Similarity NPC302310
0.6825 Remote Similarity NPC137538
0.6818 Remote Similarity NPC478095
0.6818 Remote Similarity NPC302564

  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 NPC471278 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
0.7231 Intermediate Similarity NPD4246 Clinical (unspecified phase)
0.6885 Remote Similarity NPD6927 Phase 3
0.6667 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6571 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6463 Remote Similarity NPD6082 Clinical (unspecified phase)
0.6441 Remote Similarity NPD6097 Approved
0.6441 Remote Similarity NPD6096 Approved
0.6429 Remote Similarity NPD3197 Phase 1
0.6418 Remote Similarity NPD6109 Phase 1
0.6393 Remote Similarity NPD5343 Approved
0.6389 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6333 Remote Similarity NPD39 Approved
0.629 Remote Similarity NPD4220 Pre-registration
0.625 Remote Similarity NPD5790 Clinical (unspecified phase)
0.622 Remote Similarity NPD5331 Approved
0.622 Remote Similarity NPD5332 Approved
0.6176 Remote Similarity NPD585 Clinical (unspecified phase)
0.6145 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6066 Remote Similarity NPD4265 Approved
0.6061 Remote Similarity NPD4266 Approved
0.6061 Remote Similarity NPD3194 Approved
0.6061 Remote Similarity NPD3195 Phase 2
0.6061 Remote Similarity NPD3196 Approved
0.6056 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6024 Remote Similarity NPD7154 Phase 3
0.6 Remote Similarity NPD5326 Phase 3
0.6 Remote Similarity NPD5784 Clinical (unspecified phase)
0.6 Remote Similarity NPD4268 Approved
0.6 Remote Similarity NPD4271 Approved
0.5915 Remote Similarity NPD4194 Approved
0.5915 Remote Similarity NPD4193 Approved
0.5915 Remote Similarity NPD4192 Approved
0.5915 Remote Similarity NPD4191 Approved
0.5909 Remote Similarity NPD3172 Approved
0.5854 Remote Similarity NPD4819 Approved
0.5854 Remote Similarity NPD4822 Approved
0.5854 Remote Similarity NPD4820 Approved
0.5854 Remote Similarity NPD4821 Approved
0.5854 Remote Similarity NPD4252 Approved
0.5846 Remote Similarity NPD28 Approved
0.5846 Remote Similarity NPD29 Approved
0.5833 Remote Similarity NPD5362 Discontinued
0.5823 Remote Similarity NPD8039 Approved
0.5806 Remote Similarity NPD4222 Approved
0.5795 Remote Similarity NPD6051 Approved
0.5781 Remote Similarity NPD3173 Approved
0.5747 Remote Similarity NPD4250 Approved
0.5747 Remote Similarity NPD4251 Approved
0.5735 Remote Similarity NPD4627 Clinical (unspecified phase)
0.573 Remote Similarity NPD5785 Approved
0.573 Remote Similarity NPD7838 Discovery
0.5714 Remote Similarity NPD4270 Approved
0.5714 Remote Similarity NPD4269 Approved
0.5652 Remote Similarity NPD4219 Approved
0.5632 Remote Similarity NPD5786 Approved
0.5632 Remote Similarity NPD4249 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