Structure

Physi-Chem Properties

Molecular Weight:  300.21
Volume:  353.601
LogP:  4.514
LogD:  3.528
LogS:  -4.421
# Rotatable Bonds:  13
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.182
Synthetic Accessibility Score:  3.605
Fsp3:  0.55
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.702
MDCK Permeability:  2.155767651856877e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.743
20% Bioavailability (F20%):  0.958
30% Bioavailability (F30%):  0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.234
Plasma Protein Binding (PPB):  98.50926971435547%
Volume Distribution (VD):  1.333
Pgp-substrate:  0.9070712327957153%

ADMET: Metabolism

CYP1A2-inhibitor:  0.723
CYP1A2-substrate:  0.191
CYP2C19-inhibitor:  0.86
CYP2C19-substrate:  0.443
CYP2C9-inhibitor:  0.732
CYP2C9-substrate:  0.983
CYP2D6-inhibitor:  0.625
CYP2D6-substrate:  0.192
CYP3A4-inhibitor:  0.705
CYP3A4-substrate:  0.097

ADMET: Excretion

Clearance (CL):  2.97
Half-life (T1/2):  0.318

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.313
Drug-inuced Liver Injury (DILI):  0.867
AMES Toxicity:  0.255
Rat Oral Acute Toxicity:  0.955
Maximum Recommended Daily Dose:  0.991
Skin Sensitization:  0.969
Carcinogencity:  0.422
Eye Corrosion:  0.933
Eye Irritation:  0.982
Respiratory Toxicity:  0.986

Download Data

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

  Natural Product: NPC471239

Natural Product ID:  NPC471239
Common Name*:   (4E,16E)-18-Hydroxyicosa-4,16-Dien-1,19-Diyn-3-One
IUPAC Name:   (4E,16E)-18-hydroxyicosa-4,16-dien-1,19-diyn-3-one
Synonyms:  
Standard InCHIKey:  GGYYBTJLJDDYPT-YTEMWHBBSA-N
Standard InCHI:  InChI=1S/C20H28O2/c1-3-19(21)17-15-13-11-9-7-5-6-8-10-12-14-16-18-20(22)4-2/h1-2,15-19,21H,5-14H2/b17-15+,18-16+
SMILES:  C#CC(C=CCCCCCCCCCCC=CC(=O)C#C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2407104
PubChem CID:   71745534
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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Activity = 78.0 % PMID[535952]

☑ 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 NPC471239 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
0.9057 High Similarity NPC48058
0.8947 High Similarity NPC168407
0.8824 High Similarity NPC471275
0.8824 High Similarity NPC471280
0.8824 High Similarity NPC125122
0.8824 High Similarity NPC471276
0.8654 High Similarity NPC477727
0.8654 High Similarity NPC471281
0.8654 High Similarity NPC199286
0.8545 High Similarity NPC470963
0.8545 High Similarity NPC146551
0.8545 High Similarity NPC474513
0.8491 Intermediate Similarity NPC89824
0.8491 Intermediate Similarity NPC9273
0.8491 Intermediate Similarity NPC76198
0.8491 Intermediate Similarity NPC55383
0.8491 Intermediate Similarity NPC329608
0.8491 Intermediate Similarity NPC224148
0.8491 Intermediate Similarity NPC170776
0.8491 Intermediate Similarity NPC256656
0.8491 Intermediate Similarity NPC197272
0.8491 Intermediate Similarity NPC165447
0.8491 Intermediate Similarity NPC471959
0.8491 Intermediate Similarity NPC294278
0.8491 Intermediate Similarity NPC477723
0.8491 Intermediate Similarity NPC475477
0.8462 Intermediate Similarity NPC248884
0.8462 Intermediate Similarity NPC31194
0.8462 Intermediate Similarity NPC85079
0.8431 Intermediate Similarity NPC35141
0.8431 Intermediate Similarity NPC124183
0.8393 Intermediate Similarity NPC470964
0.8393 Intermediate Similarity NPC311648
0.8302 Intermediate Similarity NPC72699
0.8302 Intermediate Similarity NPC474642
0.8302 Intermediate Similarity NPC473913
0.8302 Intermediate Similarity NPC249670
0.8276 Intermediate Similarity NPC473652
0.8246 Intermediate Similarity NPC48968
0.8246 Intermediate Similarity NPC193975
0.8246 Intermediate Similarity NPC594
0.8214 Intermediate Similarity NPC152668
0.8148 Intermediate Similarity NPC151782
0.8113 Intermediate Similarity NPC153538
0.8077 Intermediate Similarity NPC19834
0.8077 Intermediate Similarity NPC55063
0.8039 Intermediate Similarity NPC101616
0.8036 Intermediate Similarity NPC473532
0.7937 Intermediate Similarity NPC473752
0.7925 Intermediate Similarity NPC471958
0.7895 Intermediate Similarity NPC475353
0.7895 Intermediate Similarity NPC477725
0.7895 Intermediate Similarity NPC477726
0.7895 Intermediate Similarity NPC473721
0.7895 Intermediate Similarity NPC473735
0.7895 Intermediate Similarity NPC473910
0.7895 Intermediate Similarity NPC473896
0.7895 Intermediate Similarity NPC473725
0.7885 Intermediate Similarity NPC269074
0.7857 Intermediate Similarity NPC61177
0.7833 Intermediate Similarity NPC471278
0.7818 Intermediate Similarity NPC93639
0.7759 Intermediate Similarity NPC475384
0.7759 Intermediate Similarity NPC470967
0.7759 Intermediate Similarity NPC473847
0.7759 Intermediate Similarity NPC470966
0.7759 Intermediate Similarity NPC477661
0.7759 Intermediate Similarity NPC470969
0.7759 Intermediate Similarity NPC470968
0.7759 Intermediate Similarity NPC471960
0.7759 Intermediate Similarity NPC161838
0.7719 Intermediate Similarity NPC256209
0.7719 Intermediate Similarity NPC49059
0.7705 Intermediate Similarity NPC475984
0.7692 Intermediate Similarity NPC145755
0.7692 Intermediate Similarity NPC267514
0.7679 Intermediate Similarity NPC142092
0.7647 Intermediate Similarity NPC149668
0.7627 Intermediate Similarity NPC265551
0.7627 Intermediate Similarity NPC470970
0.7627 Intermediate Similarity NPC212730
0.7586 Intermediate Similarity NPC474644
0.7586 Intermediate Similarity NPC317899
0.7581 Intermediate Similarity NPC470965
0.7547 Intermediate Similarity NPC474362
0.7547 Intermediate Similarity NPC474202
0.75 Intermediate Similarity NPC129263
0.75 Intermediate Similarity NPC59408
0.75 Intermediate Similarity NPC71053
0.7458 Intermediate Similarity NPC474643
0.7458 Intermediate Similarity NPC473865
0.7419 Intermediate Similarity NPC66460
0.7419 Intermediate Similarity NPC271282
0.7419 Intermediate Similarity NPC325929
0.7414 Intermediate Similarity NPC300121
0.7414 Intermediate Similarity NPC110732
0.7407 Intermediate Similarity NPC157096
0.7407 Intermediate Similarity NPC180575
0.7333 Intermediate Similarity NPC44542
0.7321 Intermediate Similarity NPC20934
0.7321 Intermediate Similarity NPC288381
0.7321 Intermediate Similarity NPC291437
0.7321 Intermediate Similarity NPC328784
0.7308 Intermediate Similarity NPC304151
0.7302 Intermediate Similarity NPC29697
0.7255 Intermediate Similarity NPC329762
0.7255 Intermediate Similarity NPC27444
0.7255 Intermediate Similarity NPC103236
0.7241 Intermediate Similarity NPC187361
0.7241 Intermediate Similarity NPC26102
0.7241 Intermediate Similarity NPC477724
0.7241 Intermediate Similarity NPC34577
0.7241 Intermediate Similarity NPC284224
0.7167 Intermediate Similarity NPC324224
0.7167 Intermediate Similarity NPC472808
0.7143 Intermediate Similarity NPC302310
0.7119 Intermediate Similarity NPC189677
0.7115 Intermediate Similarity NPC7754
0.7115 Intermediate Similarity NPC270170
0.7069 Intermediate Similarity NPC473705
0.7049 Intermediate Similarity NPC471279
0.7049 Intermediate Similarity NPC71755
0.7049 Intermediate Similarity NPC471277
0.7049 Intermediate Similarity NPC472445
0.7037 Intermediate Similarity NPC108195
0.7018 Intermediate Similarity NPC474391
0.6949 Remote Similarity NPC217188
0.6923 Remote Similarity NPC226592
0.6923 Remote Similarity NPC470320
0.6912 Remote Similarity NPC143396
0.6897 Remote Similarity NPC473672
0.6897 Remote Similarity NPC474495
0.6875 Remote Similarity NPC477829
0.6875 Remote Similarity NPC26810
0.6866 Remote Similarity NPC225272
0.6842 Remote Similarity NPC267110
0.6825 Remote Similarity NPC222852
0.6774 Remote Similarity NPC268185
0.6731 Remote Similarity NPC217923
0.6731 Remote Similarity NPC15934
0.6724 Remote Similarity NPC225974
0.6724 Remote Similarity NPC473768
0.6724 Remote Similarity NPC473487
0.6667 Remote Similarity NPC206906
0.6667 Remote Similarity NPC67920
0.6667 Remote Similarity NPC287397
0.6667 Remote Similarity NPC236208
0.6667 Remote Similarity NPC216416
0.6667 Remote Similarity NPC298710
0.6618 Remote Similarity NPC106613
0.661 Remote Similarity NPC477458
0.6607 Remote Similarity NPC276825
0.6571 Remote Similarity NPC286154
0.6567 Remote Similarity NPC296436
0.6567 Remote Similarity NPC176215
0.6562 Remote Similarity NPC474267
0.6557 Remote Similarity NPC269615
0.6552 Remote Similarity NPC475153
0.6522 Remote Similarity NPC117804
0.6508 Remote Similarity NPC129150
0.6481 Remote Similarity NPC33489
0.6479 Remote Similarity NPC95863
0.6479 Remote Similarity NPC319163
0.6479 Remote Similarity NPC474884
0.6479 Remote Similarity NPC67076
0.6471 Remote Similarity NPC83965
0.6471 Remote Similarity NPC146811
0.6471 Remote Similarity NPC213767
0.6462 Remote Similarity NPC235242
0.6462 Remote Similarity NPC327112
0.6441 Remote Similarity NPC475071
0.6438 Remote Similarity NPC260396
0.6406 Remote Similarity NPC223679
0.6406 Remote Similarity NPC469373
0.6393 Remote Similarity NPC474496
0.6389 Remote Similarity NPC329890
0.6379 Remote Similarity NPC324812
0.6377 Remote Similarity NPC122627
0.6364 Remote Similarity NPC269737
0.6364 Remote Similarity NPC150502
0.6364 Remote Similarity NPC260573
0.6338 Remote Similarity NPC476037
0.6333 Remote Similarity NPC29234
0.6324 Remote Similarity NPC19769
0.6324 Remote Similarity NPC245947
0.6324 Remote Similarity NPC96414
0.6324 Remote Similarity NPC136164
0.6324 Remote Similarity NPC7940
0.6324 Remote Similarity NPC255863
0.6308 Remote Similarity NPC22897
0.6308 Remote Similarity NPC159650
0.6308 Remote Similarity NPC97570
0.6308 Remote Similarity NPC329424
0.6301 Remote Similarity NPC227396
0.6301 Remote Similarity NPC144995
0.6301 Remote Similarity NPC227814
0.6269 Remote Similarity NPC44343
0.6269 Remote Similarity NPC210303
0.6269 Remote Similarity NPC179087
0.6267 Remote Similarity NPC476007

  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 NPC471239 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
0.6721 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6462 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6271 Remote Similarity NPD4220 Pre-registration
0.6034 Remote Similarity NPD4265 Approved
0.6029 Remote Similarity NPD3210 Clinical (unspecified phase)
0.5882 Remote Similarity NPD4193 Approved
0.5882 Remote Similarity NPD4194 Approved
0.5882 Remote Similarity NPD4191 Approved
0.5882 Remote Similarity NPD4192 Approved
0.5846 Remote Similarity NPD4219 Approved
0.5714 Remote Similarity NPD3197 Phase 1
0.5694 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5663 Remote Similarity NPD5363 Approved
0.5634 Remote Similarity NPD2685 Clinical (unspecified phase)
0.561 Remote Similarity NPD5331 Approved
0.561 Remote Similarity NPD5332 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