Structure

Physi-Chem Properties

Molecular Weight:  256.07
Volume:  259.033
LogP:  3.086
LogD:  2.637
LogS:  -3.39
# Rotatable Bonds:  1
TPSA:  70.67
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.656
Synthetic Accessibility Score:  2.448
Fsp3:  0.133
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.885
MDCK Permeability:  7.56671215640381e-06
Pgp-inhibitor:  0.002
Pgp-substrate:  0.988
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.023
30% Bioavailability (F30%):  0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.046
Plasma Protein Binding (PPB):  91.93653869628906%
Volume Distribution (VD):  0.669
Pgp-substrate:  8.190200805664062%

ADMET: Metabolism

CYP1A2-inhibitor:  0.976
CYP1A2-substrate:  0.851
CYP2C19-inhibitor:  0.309
CYP2C19-substrate:  0.105
CYP2C9-inhibitor:  0.519
CYP2C9-substrate:  0.792
CYP2D6-inhibitor:  0.775
CYP2D6-substrate:  0.774
CYP3A4-inhibitor:  0.344
CYP3A4-substrate:  0.196

ADMET: Excretion

Clearance (CL):  1.926
Half-life (T1/2):  0.817

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.089
Drug-inuced Liver Injury (DILI):  0.769
AMES Toxicity:  0.613
Rat Oral Acute Toxicity:  0.061
Maximum Recommended Daily Dose:  0.265
Skin Sensitization:  0.913
Carcinogencity:  0.611
Eye Corrosion:  0.048
Eye Irritation:  0.984
Respiratory Toxicity:  0.105

Download Data

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

  Natural Product: NPC71053

Natural Product ID:  NPC71053
Common Name*:   Oenanthotoxin
IUPAC Name:   (2E,8E,10E,14R)-heptadeca-2,8,10-trien-4,6-diyne-1,14-diol
Synonyms:   Oenanthotoxin
Standard InCHIKey:  UPXPHJXYZGEBCW-SRFVWEJJSA-N
Standard InCHI:  InChI=1S/C17H22O2/c1-2-14-17(19)15-12-10-8-6-4-3-5-7-9-11-13-16-18/h4,6,8,10-11,13,17-19H,2,12,14-16H2,1H3/b6-4+,10-8+,13-11+/t17-/m1/s1
SMILES:  CCC[C@H](CC/C=C/C=C/C#CC#C/C=C/CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL550225
PubChem CID:   44138996
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
NPO598 Oenanthe fistulosa Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[19245244]
NPO598 Oenanthe fistulosa Species Apiaceae 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
NPT81 Cell Line A549 Homo sapiens EC50 = 10900.0 nM PMID[552572]
NPT179 Cell Line A2780 Homo sapiens EC50 = 3800.0 nM PMID[552572]
NPT1215 Cell Line 8505C Homo sapiens EC50 = 10500.0 nM PMID[552572]
NPT139 Cell Line HT-29 Homo sapiens EC50 > 30000.0 nM PMID[552572]
NPT83 Cell Line MCF7 Homo sapiens EC50 = 20600.0 nM PMID[552572]
NPT2 Others Unspecified EC50 = 1390.0 nM PMID[552571]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. EC50 = 17100.0 nM PMID[552572]
NPT27 Others Unspecified EC50 = 10100.0 nM PMID[552572]

☑ 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 NPC71053 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 NPC59408
0.94 High Similarity NPC110732
0.9375 High Similarity NPC328784
0.9375 High Similarity NPC291437
0.9184 High Similarity NPC151782
0.9167 High Similarity NPC302310
0.9167 High Similarity NPC153538
0.898 High Similarity NPC72699
0.88 High Similarity NPC93639
0.8776 High Similarity NPC248884
0.8776 High Similarity NPC31194
0.8776 High Similarity NPC85079
0.875 High Similarity NPC124183
0.875 High Similarity NPC35141
0.875 High Similarity NPC180575
0.8654 High Similarity NPC256209
0.8654 High Similarity NPC49059
0.8542 High Similarity NPC276825
0.8519 High Similarity NPC44542
0.8462 Intermediate Similarity NPC61177
0.8462 Intermediate Similarity NPC34577
0.84 Intermediate Similarity NPC471280
0.84 Intermediate Similarity NPC125122
0.84 Intermediate Similarity NPC471275
0.84 Intermediate Similarity NPC471276
0.8367 Intermediate Similarity NPC19834
0.8367 Intermediate Similarity NPC55063
0.8333 Intermediate Similarity NPC101616
0.8302 Intermediate Similarity NPC473532
0.8298 Intermediate Similarity NPC206906
0.8269 Intermediate Similarity NPC142092
0.8235 Intermediate Similarity NPC473913
0.8235 Intermediate Similarity NPC477727
0.8235 Intermediate Similarity NPC471281
0.8235 Intermediate Similarity NPC474642
0.8235 Intermediate Similarity NPC249670
0.8235 Intermediate Similarity NPC199286
0.8214 Intermediate Similarity NPC222852
0.8182 Intermediate Similarity NPC472445
0.8163 Intermediate Similarity NPC269074
0.8148 Intermediate Similarity NPC473896
0.8148 Intermediate Similarity NPC473725
0.8148 Intermediate Similarity NPC473910
0.8148 Intermediate Similarity NPC477725
0.8148 Intermediate Similarity NPC477726
0.8148 Intermediate Similarity NPC473735
0.8148 Intermediate Similarity NPC473721
0.8148 Intermediate Similarity NPC475353
0.8113 Intermediate Similarity NPC284224
0.8077 Intermediate Similarity NPC76198
0.8077 Intermediate Similarity NPC197272
0.8077 Intermediate Similarity NPC129263
0.8077 Intermediate Similarity NPC471959
0.8077 Intermediate Similarity NPC256656
0.8077 Intermediate Similarity NPC170776
0.8077 Intermediate Similarity NPC165447
0.8077 Intermediate Similarity NPC294278
0.8077 Intermediate Similarity NPC89824
0.8077 Intermediate Similarity NPC329608
0.8077 Intermediate Similarity NPC9273
0.8077 Intermediate Similarity NPC475477
0.8077 Intermediate Similarity NPC474495
0.8077 Intermediate Similarity NPC224148
0.8077 Intermediate Similarity NPC477723
0.8077 Intermediate Similarity NPC55383
0.8077 Intermediate Similarity NPC473672
0.8 Intermediate Similarity NPC470967
0.8 Intermediate Similarity NPC473847
0.8 Intermediate Similarity NPC470969
0.8 Intermediate Similarity NPC470968
0.8 Intermediate Similarity NPC161838
0.8 Intermediate Similarity NPC477661
0.8 Intermediate Similarity NPC471960
0.8 Intermediate Similarity NPC470966
0.8 Intermediate Similarity NPC475384
0.7959 Intermediate Similarity NPC108195
0.7917 Intermediate Similarity NPC304151
0.7857 Intermediate Similarity NPC193975
0.7857 Intermediate Similarity NPC470970
0.7818 Intermediate Similarity NPC329686
0.7778 Intermediate Similarity NPC474496
0.7759 Intermediate Similarity NPC327112
0.7679 Intermediate Similarity NPC324224
0.7679 Intermediate Similarity NPC472808
0.766 Intermediate Similarity NPC15934
0.7647 Intermediate Similarity NPC157096
0.7636 Intermediate Similarity NPC48058
0.76 Intermediate Similarity NPC138935
0.7593 Intermediate Similarity NPC35756
0.7551 Intermediate Similarity NPC46248
0.7551 Intermediate Similarity NPC249801
0.7547 Intermediate Similarity NPC474460
0.7544 Intermediate Similarity NPC212730
0.7544 Intermediate Similarity NPC265551
0.75 Intermediate Similarity NPC470963
0.75 Intermediate Similarity NPC474513
0.75 Intermediate Similarity NPC471239
0.75 Intermediate Similarity NPC317899
0.75 Intermediate Similarity NPC474644
0.75 Intermediate Similarity NPC29697
0.75 Intermediate Similarity NPC146551
0.75 Intermediate Similarity NPC152668
0.7455 Intermediate Similarity NPC187361
0.7455 Intermediate Similarity NPC477724
0.7455 Intermediate Similarity NPC26102
0.7455 Intermediate Similarity NPC217188
0.7451 Intermediate Similarity NPC140501
0.7414 Intermediate Similarity NPC181872
0.7407 Intermediate Similarity NPC29234
0.74 Intermediate Similarity NPC116934
0.7377 Intermediate Similarity NPC470320
0.7368 Intermediate Similarity NPC473865
0.7368 Intermediate Similarity NPC474643
0.7368 Intermediate Similarity NPC470964
0.7368 Intermediate Similarity NPC311648
0.7333 Intermediate Similarity NPC271282
0.7333 Intermediate Similarity NPC325929
0.7333 Intermediate Similarity NPC66460
0.7333 Intermediate Similarity NPC475984
0.7321 Intermediate Similarity NPC300121
0.7288 Intermediate Similarity NPC322002
0.7288 Intermediate Similarity NPC318306
0.7288 Intermediate Similarity NPC322186
0.7258 Intermediate Similarity NPC255863
0.7258 Intermediate Similarity NPC136164
0.7258 Intermediate Similarity NPC245947
0.7258 Intermediate Similarity NPC308844
0.7241 Intermediate Similarity NPC48968
0.7241 Intermediate Similarity NPC594
0.7222 Intermediate Similarity NPC473768
0.7222 Intermediate Similarity NPC20934
0.7222 Intermediate Similarity NPC288381
0.7213 Intermediate Similarity NPC470965
0.72 Intermediate Similarity NPC149668
0.7193 Intermediate Similarity NPC227135
0.7167 Intermediate Similarity NPC328311
0.7167 Intermediate Similarity NPC471278
0.7143 Intermediate Similarity NPC329762
0.7143 Intermediate Similarity NPC27444
0.7143 Intermediate Similarity NPC103236
0.7119 Intermediate Similarity NPC226848
0.7115 Intermediate Similarity NPC160628
0.7115 Intermediate Similarity NPC76976
0.7097 Intermediate Similarity NPC226592
0.7083 Intermediate Similarity NPC34873
0.7083 Intermediate Similarity NPC40434
0.7059 Intermediate Similarity NPC252978
0.7049 Intermediate Similarity NPC477829
0.7037 Intermediate Similarity NPC267110
0.7021 Intermediate Similarity NPC79544
0.7 Intermediate Similarity NPC122239
0.7 Intermediate Similarity NPC475931
0.7 Intermediate Similarity NPC269823
0.7 Intermediate Similarity NPC473652
0.7 Intermediate Similarity NPC329249
0.6984 Remote Similarity NPC323045
0.6984 Remote Similarity NPC317881
0.6964 Remote Similarity NPC473705
0.6964 Remote Similarity NPC106531
0.6949 Remote Similarity NPC121034
0.6939 Remote Similarity NPC103213
0.6939 Remote Similarity NPC29091
0.6939 Remote Similarity NPC182840
0.6939 Remote Similarity NPC306850
0.6939 Remote Similarity NPC255042
0.6935 Remote Similarity NPC471023
0.6935 Remote Similarity NPC55068
0.6909 Remote Similarity NPC475071
0.6909 Remote Similarity NPC473487
0.6897 Remote Similarity NPC232247
0.6897 Remote Similarity NPC251666
0.6897 Remote Similarity NPC474913
0.6875 Remote Similarity NPC146811
0.6863 Remote Similarity NPC213538
0.6863 Remote Similarity NPC256766
0.6833 Remote Similarity NPC469373
0.6833 Remote Similarity NPC155025
0.6818 Remote Similarity NPC236208
0.6818 Remote Similarity NPC143396
0.6809 Remote Similarity NPC58957
0.6786 Remote Similarity NPC200772
0.678 Remote Similarity NPC55412
0.678 Remote Similarity NPC48891
0.678 Remote Similarity NPC249645
0.6774 Remote Similarity NPC168407
0.6774 Remote Similarity NPC26810
0.6774 Remote Similarity NPC225342
0.6774 Remote Similarity NPC113293
0.6769 Remote Similarity NPC49863
0.6727 Remote Similarity NPC475153
0.6724 Remote Similarity NPC189677
0.6724 Remote Similarity NPC269615
0.6721 Remote Similarity NPC473866
0.6719 Remote Similarity NPC323477
0.6719 Remote Similarity NPC318420
0.6719 Remote Similarity NPC326268
0.6716 Remote Similarity NPC476037
0.6667 Remote Similarity NPC474577
0.6667 Remote Similarity NPC208638
0.6667 Remote Similarity NPC71755

  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 NPC71053 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
0.7759 Intermediate Similarity NPD4246 Clinical (unspecified phase)
0.7451 Intermediate Similarity NPD4265 Approved
0.6935 Remote Similarity NPD3210 Clinical (unspecified phase)
0.678 Remote Similarity NPD4219 Approved
0.6769 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6557 Remote Similarity NPD585 Clinical (unspecified phase)
0.6522 Remote Similarity NPD4732 Discontinued
0.6508 Remote Similarity NPD368 Approved
0.6429 Remote Similarity NPD4220 Pre-registration
0.6338 Remote Similarity NPD8264 Approved
0.6333 Remote Similarity NPD342 Phase 1
0.6232 Remote Similarity NPD3212 Clinical (unspecified phase)
0.6182 Remote Similarity NPD39 Approved
0.6081 Remote Similarity NPD7322 Clinical (unspecified phase)
0.6061 Remote Similarity NPD3197 Phase 1
0.5921 Remote Similarity NPD7332 Phase 2
0.5921 Remote Similarity NPD7514 Phase 3
0.5893 Remote Similarity NPD4222 Approved
0.5867 Remote Similarity NPD7145 Approved
0.5862 Remote Similarity NPD3173 Approved
0.5844 Remote Similarity NPD6898 Phase 1
0.5844 Remote Similarity NPD6902 Approved
0.5818 Remote Similarity NPD5326 Phase 3
0.5781 Remote Similarity NPD6109 Phase 1
0.5775 Remote Similarity NPD7144 Approved
0.5775 Remote Similarity NPD7143 Approved
0.5758 Remote Similarity NPD4191 Approved
0.5758 Remote Similarity NPD4193 Approved
0.5758 Remote Similarity NPD4194 Approved
0.5758 Remote Similarity NPD4192 Approved
0.5738 Remote Similarity NPD3172 Approved
0.5733 Remote Similarity NPD6925 Approved
0.5733 Remote Similarity NPD5776 Phase 2
0.5696 Remote Similarity NPD5332 Approved
0.5696 Remote Similarity NPD5331 Approved
0.5694 Remote Similarity NPD7150 Approved
0.5694 Remote Similarity NPD7151 Approved
0.5694 Remote Similarity NPD7152 Approved
0.5658 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5658 Remote Similarity NPD4268 Approved
0.5658 Remote Similarity NPD4271 Approved
0.5645 Remote Similarity NPD4266 Approved
0.5645 Remote Similarity NPD3194 Approved
0.5645 Remote Similarity NPD3195 Phase 2
0.5645 Remote Similarity NPD3196 Approved
0.5634 Remote Similarity NPD6923 Approved
0.5634 Remote Similarity NPD6922 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